Digestive

Digestive System Subsection (40490-49999) Overview

The Digestive System subsection is divided based on anatomic sites, ranging from the mouth to the anus, and includes the internal organs involved in digestion, such as the pancreas, liver, and gallbladder. This section also includes codes for procedures related to the abdomen, peritoneum, omentum, and hernia repairs. Endoscopic codes are dispersed throughout this subsection according to anatomical location.

Lips (40490-40799)

The codes under the Lips subheading cover procedures such as Excision, Repair (Cheiloplasty), and Other Procedures. If the procedure was performed on the skin of the lips, a code from the Integumentary System should be used instead of one from the Digestive System.

Vermilionectomy (40500): A procedure where the surgeon shaves the red part of the lips (the vermilion zone) to remove a portion of the tissue and repair the defect by advancing the mucosal surface to reconnect the lip. For larger defects, more extensive excision procedures, such as the Transverse Wedge Excision (40510), may be required. These procedures often involve removing a wedge of tissue and using tissue flaps to repair the lip.

For full-thickness excisions, codes like 40525 are used, which describe excisions with local flap reconstruction. Several services are bundled under this code, including:

  • Benign lesion excisions (11440-11444, 11446)

  • Malignant lesion excisions (11640-11644, 11646)

  • Vermilionectomy with mucosal advancement (40500)

  • Lip excisions (40510, 40520)

Abbe-Estlander Flap (40527): A reconstructive procedure where a graft is taken from a portion of the lip and a flap above the lip is used to repair a defect. This procedure is particularly useful when a part of the lip is removed due to cancer (e.g., caused by smoking). If more than a quarter of the lip is removed, the procedure is considered a resection (40530) and may require additional reconstruction procedures reported separately.

Repair Codes for Lip Procedures (40650-40761)

These codes are used for lip repairs. There are two categories:

  1. Full-thickness lip repairs (40650-40654): These codes depend on the extent of the repair, such as:

    • Vermilion only (40650)

    • Half of the vertical height of the lip (40652)

    • Over half of the vertical height (40654 for complex repair)

  2. Cleft Lip Repairs (40700-40761): These codes address repairs for congenital defects where the muscle and tissue of the lip did not close properly. The procedure can be bilateral or unilateral, depending on the defect. If a bilateral procedure is performed and the code does not specify it, modifier -50 should be added.

Additional Procedures

  • Rhinoplasty: Sometimes required if nasal deformities occur alongside a cleft lip. The codes 30460 and 30462 are used for rhinoplasties performed separately.

  • Cleft Palate Repair: A cleft palate may accompany a cleft lip, and if repair is done simultaneously, it is reported with codes from the 42200 series, such as 42205, which addresses a palatoplasty for cleft palate closure.

  1. An Abbe-Estlander flap is also known as an Abbe or cross flap.


Vestibule of Mouth (40800-40899)

The vestibule of the mouth, also known as the buccal cavity, is part of the oral cavity. Codes for procedures performed in this area do not include services for the Tongue, Floor of Mouth, or Dentoalveolar Structures. The codes under the Vestibule of Mouth subheading cover:

  • Incisions (e.g., abscess, cyst, or hematoma)

  • Excision/Destruction (e.g., biopsy or lesion excision)

  • Repair (e.g., closure or vestibuloplasty)

Procedures are categorized based on complexity (simple or complex) and whether they are bilateral or unilateral.

Tongue and Floor of Mouth (41000-41599)

The Tongue and Floor of Mouth subheading includes codes for:

  • Incision and drainage of abscesses, cysts, or hematomas

  • Procedures are based on the location of the abscess, cyst, or hematoma, such as:

    • Sublingual (under the tongue)

    • Submandibular (under the mandible)

    • Masticator space (from the floor of the mouth to the hyoid bone)

The lingual frenum is the flap of skin under the tongue. Ankyloglossia (tongue tie), a condition where the lingual frenum is tight, affects about 4.8% of the population and can interfere with feeding in infants.

  • Frenotomy (41010): An incision made in the lingual frenum to free the tongue for better motion. This procedure involves only incising the frenum, not excising it.

  • Frenectomy (41115): A more extensive procedure where the lingual frenum is excised.

  • Frenoplasty (41520): A surgical repair of the lingual frenum.

Extraoral Incision and Drainage (I&D)

Codes 41015-41018 report extraoral incision and drainage procedures performed outside the mouth, including locations like:

  • Sublingual (under the tongue)

  • Submental (under the chin)

  • Submandibular

  • Masticator space (deep facial space containing muscles of mastication, ramus, and posterior body of the mandible)

Excision Codes for Tongue and Floor of Mouth (41100-41155)

These codes cover:

  • Oral biopsies

  • Excision of oral lesions

  • Glossectomy (removal of all or part of the tongue)

The biopsy codes (41100-41108) depend on the location of the biopsy. Similarly, excision codes are based on the lesion's location (e.g., floor of mouth, tongue, or lingual frenum). If a local tongue flap is needed to repair the excision, the repair is coded with 41114 in addition to the excision code.

Repair Codes for Tongue (41250-41252)

Repair of the tongue is based on:

  • Size of the repair (≤ 2.5 cm or > 2.6 cm)

  • Location of the repair (e.g., floor of the mouth, anterior two-thirds of the tongue, or posterior one-third of the tongue)

When measurements are provided in inches, they must be converted to centimeters. The conversion formulas are:

  • Centimeters × 0.3937008 = inches

  • Inches × 2.54 = centimeters

For millimeters (mm), the conversion is:

  • 1 millimeter = 0.1 centimeters

For example, 15 millimeters = 15 × 0.1 = 1.5 centimeters.

Dentoalveolar Structures (41800-41899)

The dentoalveolar structures consist of the bone and soft tissues that anchor the teeth in the mouth. Codes in this range cover:

  • Incision, Excision/Destruction, and other procedures on the dentoalveolar structures.

  • Examples of these procedures include:

    • Abscess drainage (41800)

    • Excision of lesions with simple repair (41826)

    • Excision of gingiva (gingivectomy) and alveolar mucosa, often reported per quadrant (41820 for gingivectomy, 41828 for alveolar mucosa excision)

These codes depend on the location of the procedure, with some procedures being performed on each quadrant of the mouth.

Palate and Uvula (42000-42299)

Services related to the palate (roof of the mouth) and uvula (pendulous structure at the back of the throat) are reported under this subheading, including:

  • Incision

  • Excision/Destruction

  • Repair

When grafting is necessary to repair a defect after excision, the grafting service is reported in addition to the excision code. The choice of grafting codes depends on the type of graft used:

  • Skin graft: Codes 14040-14302

  • Oral mucosal graft: Code 40818

The Repair codes (42200-42225) also cover cleft palate repairs, as discussed earlier.

Palatopharyngoplasty (42145)

The palatopharyngoplasty is a procedure described by code 42145 that involves repairing both the palate and pharynx. It is primarily indicated for patients with obstructive sleep apnea (OSA) that does not respond to conservative treatments such as CPAP (continuous positive airway pressure), positional therapy, dental devices, or weight loss. OSA is marked by episodes of shallow breathing (hypopnea) or complete cessation of breathing (apnea) during sleep.

Salivary Glands and Ducts (42300-42699)

There are three main salivary glands:

  • Parotid (located near the ear)

  • Submandibular (under the jaw)

  • Sublingual (under the tongue)

Salivary Gland Biopsy

The biopsy codes for the salivary glands are:

  • 42400: Needle biopsy of the salivary gland

  • 42405: Incisional biopsy of the salivary gland

For procedures involving sialography (an X-ray of the salivary glands), use code 42550. The radiological component of this procedure is reported separately with 70390. It's important to refer to any parenthetical statements in the CPT manual that may indicate additional services to be reported, such as radiological supervision and interpretation.

If imaging guidance is used during a biopsy, it should be reported in addition to the biopsy service. The types of imaging guidance codes include:

  • 77002: Fluoroscopic guidance

  • 77012: CT guidance

  • 77021: MRI guidance

  • 76942: Ultrasound guidance

Excision of Tumors in Salivary Glands

Excision of tumors from specific salivary glands is coded as follows:

  • Parotid gland: 42410

  • Submandibular gland: 42440

  • Sublingual gland: 42450

For excision involving multiple glands, the number of glands involved determines the code used. For example, when both the parotid duct (also known as Steno’s duct) and submandibular glands are involved, the procedure for both the diversion and excision is reported with 42509.

The parotid duct is the duct opening from the cheek into the vestibule of the mouth, located opposite the neck of the upper second molar tooth.


Pharynx, Adenoids, and Tonsils (42700-42999)

This section covers procedures related to the pharynx, adenoids, and tonsils. Codes in this range are commonly used for tonsillectomies, adenoidectomies, incisions, biopsies, excision, and repair.

Incision Procedures (42700-42725)

  • These codes report the drainage of abscesses located around the tonsils (peritonsillar), behind the pharynx (retropharyngeal), or adjacent to the pharynx (parapharyngeal).

  • The location and approach (intraoral or external) determine the code used. It's essential to carefully read the operative report to ensure the correct code is assigned.

Biopsy Procedures (42800-42806)

  • Biopsies of the pharynx or tonsils are reported with these codes, but they do not include the use of a scope to collect the sample.

  • If a laryngoscopic biopsy is performed, it should be reported under the Respiratory System (not Digestive).

Branchial Cleft Cyst Excision (42810-42815)

  • A branchial cleft cyst is a congenital defect resembling a gill on the neck.

    • If the defect is confined to the skin and subcutaneous tissue, use 42810.

    • If it extends beneath the subcutaneous tissue into the pharynx, use 42815.

Tonsillectomy and Adenoidectomy (42820-42836)

  • Common procedures reported within this code range include tonsillectomy (removal of tonsils) and adenoidectomy (removal of adenoids).

  • The code selection depends on:

    • Whether only tonsils are removed

    • Whether only adenoids are removed

    • Whether both tonsils and adenoids are removed

    • Age of the patient (under 12 years or 12 years and older)

    Modifier Usage:

    • -50 modifier or -RT/-LT may not be recognized by some payers for tonsillectomies and adenoidectomies and will usually be paid based on a single procedure.

    • If only one side is removed, use modifier -52 (reduced service).

Pharyngoplasty and Pharyngostomy (42950-42955)

  • Pharyngoplasty (42950): Surgical repair of the pharynx, often using flaps from nearby tissues like skin or the tongue.

    • If a pharyngeal flap is used, report with 42225.

  • Pharyngostomy (42955): Creation of an opening in the pharynx to insert a long-term feeding tube, often used in cases of severe facial trauma.

Hemorrhage Control (42960-42972)

  • Codes in this range cover procedures for controlling hemorrhage in the oropharyngeal and nasopharyngeal regions.

  • These codes are assigned based on whether the procedure is primary or secondary and the complexity of the service.

Esophagus Procedures (43020-43499)

This section covers various esophageal procedures such as incision, excision, endoscopy, repair, and manipulation.

Diagnostic and Therapeutic Endoscopy (43180-43233)

  • These codes cover endoscopic procedures limited to the esophagus, including diagnostic services like esophagoscopy and biopsy.

  • Some procedures may extend to the stomach but not reach the pylorus.

  • Examples:

    • 43191: Transoral rigid esophagoscopy

    • 43200: Flexible esophagoscopy

Excision of Lesions (43100-43135)

  • Lesions of the esophagus are removed depending on the approach:

    • 43100: Cervical approach

    • 43101: Thoracic or abdominal approach

Removal of Foreign Bodies (43020-43045)

  • Codes for foreign body removal depend on whether the approach is cervical (through the neck) or thoracic (through the chest).

  • For example, 43100 (cervical) or 43101 (thoracic or abdominal) would be used based on the surgical approach.

Dilation Procedures (43450-43460)

  • Esophageal dilation is performed for various issues like strictures, using instruments like a bougie or a guidewire.

    • Some procedures may require fluoroscopic guidance.

    • Example: 43213 reports a dilation procedure with endoscopic guidance.

Polyp or Tumor Removal (43216-43217)

  • These codes describe the removal of polyps or tumors from the esophagus.

    • Hot biopsy forceps are used to remove and cauterize lesions in a single procedure.

Submucosal Injections (43192-43201)

  • Submucosal injections help elevate polyps for easier removal. The method and delivery mechanism (e.g., esophagoscopy, sigmoidoscopy) determine the specific code.

Esophagogastroduodenoscopy (EGD) (43259-43499)

EGD is a procedure to examine the esophagus, stomach, and duodenum for abnormalities like tumors, ulcers, and bleeding.

  • 43259: Endoscopic ultrasound of the esophagus (includes the use of a scope for diagnostic purposes).

  • Additional procedures may be performed during the same session, such as dilation or biopsy. If multiple procedures are done, use modifier -51.

Coding Example: ERCP (43260-43278)

ERCP is used to diagnose and treat issues in the bile ducts, pancreatic ducts, and gallbladder. It combines endoscopy with X-ray.

  • 43260: ERCP diagnostic procedure

  • If radiology supervision is needed, report the service with:

    • 74328: For biliary ducts

    • 74329: For pancreatic ducts

    • 74330: For both

When performing ERCP, the procedure may involve specimen collection (brushing or washing), but this is included in the service and not separately reported.

Laparoscopy (43279-43289)

Laparoscopy involves a camera inserted through a small incision in the abdomen to examine the organs. It's used for both diagnostic and therapeutic purposes.

  • 43286-43288: Codes for esophagectomy, a partial or total removal of the esophagus. These are often performed with laparoscopic or thoracoscopic techniques depending on the surgical site.

This section outlines various procedures and coding considerations for digestive system surgeries, particularly focusing on the stomach and intestines, including bariatric procedures. Here's a summary and some key points:

Stomach Procedures:

  • Incisional procedures (43500-43999): These include surgeries like gastrotomy with exploration or foreign body removal. The method of performing the procedure (open vs. laparoscopic) is crucial for correct coding.

  • Gastric bypass: Techniques like Roux-en-Y gastric bypass are used to reduce stomach size or bypass part of the stomach and intestines for weight loss. The procedure can be performed either open (with a large abdominal incision) or laparoscopically (with small access ports).

  • Bariatric Surgery (43770-43775): Includes gastric restrictive procedures, such as adjustable gastric banding. The band is adjustable via a subcutaneous port, and the amount of fluid added can limit food intake.

  • Medicare policy: Bariatric surgery coverage is available for individuals with a BMI of 35 or greater with comorbidities, and the surgery must be performed at a certified center.

Intestine Procedures:

  • Colostomies: These involve the creation of an artificial opening, often bundled with major procedures. Codes for colostomy are only reported separately when stated.

  • Endoscopic procedures: Procedures are done using scopes inserted either through the mouth (for upper GI procedures) or the anus (for lower GI procedures). Code selection depends on the extent of the procedure, from diagnostic to more complex surgeries.

  • Resection of the intestine: This involves the removal of a portion of the intestine and might involve rejoining the remaining intestine (anastomosis) or creating an artificial opening (stoma).

  • Ostomies: Artificial openings formed from different parts of the intestine—colostomy (colon), ileostomy (ileum), and gastrostomy (stomach).

Key Coding Takeaways:

  1. Identify the surgical method: Open vs. laparoscopic approaches affect the code selection.

  2. Endoscopy: Correct code selection depends on the farthest extent the scope is passed and the procedures performed.

  3. Ostomies: The anatomic site from which the ostomy is created must be identified for accurate coding.



Surgical Communications:

  1. Coloproctostomy: from the colon to the rectum.

  2. Ileostomy: from the ileum to the abdominal surface.

  3. Colostomy: from the colon to the abdominal surface.

  4. Enteroenterostomy: between two portions of the intestine.

Coding Exercise:

5. Partial bowel resection with colostomy for primary, malignant neoplasm:

  • CPT Code: 44140 (Partial colectomy with colostomy)

  • ICD-10-CM Code: C18.9 (Malignant neoplasm of colon, unspecified)

6. Resection of small intestine, single resection, with anastomosis:

  • CPT Code: 44120 (Resection of small intestine, single resection, with anastomosis)

Highlights from the Appendix:

Appendectomy Codes:

  • Open Procedures:

    • 44900: Open I&D of abscess

    • 44950: Open surgical appendectomy

  • Percutaneous Procedures:

    • 49406: Percutaneous image-guided I&D of abscess

  • Laparoscopic Procedures:

    • 44970: Laparoscopic appendectomy

    • 44955: Appendectomy performed at the time of another major procedure

    • 44960: Appendectomy when appendix has ruptured or generalized peritonitis

Colon and Rectum Procedures:

  • Procedures for the colon and rectum (45000-45999) often involve complex coding. For example:

    • 45126: Pelvic exenteration for colorectal malignancy, with multiple procedures like proctectomy, hysterectomy, and more.

Endoscopic Procedures:

  • Proctosigmoidoscopy (45300-45327): Examination of the rectum and sigmoid colon.

  • Sigmoidoscopy (45330-45350): Examining the sigmoid colon and part of the descending colon.

  • Colonoscopy (45378-45398): Endoscopic examination from the rectum to the cecum or into the terminal ileum.

Coding Tips:

  • For colonoscopy, ensure you report the technique (e.g., biopsy, polypectomy) correctly.

  • Use modifier -53 if the colonoscopy is discontinued for valid reasons (e.g., equipment failure, patient instability).

  • Modifier -25 is used if a separate E/M service is performed on the same day as a minor procedure like a colonoscopy.


It looks like you're reviewing CMS guidelines for colorectal cancer screening and specific procedures related to the colon, rectum, and anus. Here's a breakdown of some of the key points and codes mentioned:

Colorectal Cancer Screening:

  1. Screening vs. Diagnostic/ Therapeutic Procedures:

    • Screening is done when no symptoms are present, and it's reported with Z12.11 (Special screening for malignant neoplasms, colon).

    • Therapeutic procedures (e.g., biopsy, ablation) are reported when a disease is found during screening. A modifier -PT is used to indicate the screening was converted into a diagnostic/therapeutic procedure.

  2. Common HCPCS Codes for Screening Procedures:

    • G0104 – Flexible sigmoidoscopy for patients ≥50 years (once every 4 years).

    • G0105 – Colonoscopy for individuals at high risk.

    • G0121 – Screening colonoscopy for patients over 50 who are not high risk.

    • G0328 – Fecal occult blood test (FOBT) for colorectal cancer screening.

    • 45378 – Diagnostic flexible colonoscopy.

  3. Modifier -PT:

    • Use when a procedure started as a screening and was converted to a diagnostic or therapeutic procedure.

  4. Virtual Colonoscopy (CT Colonography):

    • Report with 74261 and 74262 for diagnostic purposes.

    • 74263 is not covered by Medicare for screening.

Anus Procedures:

  • Abscess Treatment: Incision and drainage (I&D) is the typical procedure.

  • Seton Placement (46020): Used for anal fistulas (abnormal passages).

  • Anal Fissure Treatment: Fissurectomy (46200), excision of fissure; sphincterotomy may be bundled into the procedure.

  • Closure of Anal Fistula: Report with 46288.

  • Anoscopy (46600): Diagnostic anoscopy with dilation; other procedures such as biopsy, foreign body removal, and hemorrhage control.

Common Codes for Anal Procedures:

  • 46250 – External hemorrhoidectomy.

  • 46260 – Hemorrhoidectomy for both internal and external hemorrhoids.

  • 46500 – Injection of sclerosing solution for hemorrhoids.

Exercise 19-4 Coding (Colon & Rectum):

  1. Appendectomy for acute ruptured appendix with generalized peritonitis – CPT Code: 44950, ICD-10-CM: K35.2

  2. Flexible Sigmoidoscopy with biopsies – CPT Code: 45330

  3. Colonoscopy with removal of polyp by snare – CPT Code: 45385

  4. Sigmoidoscopy with removal of polyps and biopsy – CPT Code: 45330


This section provides an overview of coding for various abdominal, liver, pancreas, biliary tract, and hernia-related procedures. Here are some key points for coding:

Liver Procedures

  1. Liver Biopsy

    • Percutaneous biopsy: 47000

    • Biopsy at the time of another procedure: 47001 (Add-on code)

    • Wedge biopsy: 47100 (Removal of a fan-shaped section of liver tissue)

  2. Liver Transplantation

    • Complex procedure, where each part of the transplant (graft retrieval, backbench work, transplantation) is reported separately (CPT codes 47133-47147).

Biliary Tract Procedures

  1. Incisional Procedures

    • Hepaticotomy or Hepaticostomy (exploration of the tract): 47400

    • Choledochotomy (incision into the biliary tract) and Cholecystostomy (formation of a stoma): Codes between 47400-47490

  2. Injection Procedures

    • Injection to assess biliary obstruction:

      • Percutaneous via existing access: 47531

      • Percutaneous via new access: 47532

      • These codes include imaging guidance.

  3. Laparoscopic Cholecystectomy

    • Removal of the gallbladder laparoscopically: 47562

    • Open approach for gallbladder removal (when laparoscopic fails): 47605

    • Conversion from laparoscopic to open: Only report the successful approach.

Pancreas Procedures

  1. Pancreatic Biopsy

    • Open biopsy: 48100

    • Percutaneous biopsy: 48102 (Add-on code for guidance based on method used)

  2. Pancreatic Surgery

    • Removal of the pancreas (total or partial) is reported with codes 48140-48160 based on the extent of surgery performed.

  3. Pancreatic Transplantation

    • For pancreas grafts from cadaver or living donors: 48550-48554

  4. Pancreatic Draining Procedures

    • Drain placement for pancreatitis or other fluid buildup: 48000

    • Additional procedures like cholecystostomy or gastrostomy: 48001

Abdomen and Peritoneum Procedures

  1. Diagnostic Laparoscopy

    • If laparoscopic exploration is part of a surgical procedure, it is included and not reported separately.

    • If diagnostic laparoscopy converts to a surgical procedure (e.g., draining lymphocele), report the surgical laparoscopy code: 49323

  2. Hernia Repair

    • Codes for hernia repair vary based on hernia type (epigastric, inguinal, umbilical, etc.), whether the repair is initial or recurrent, and whether it is reducible, incarcerated, or strangulated.

    • Common hernia repair codes include:

      • 49591-49596 for open repairs

      • 49613-49618 for laparoscopic repairs

      • Laparoscopic/robotic hernia repair: 49650-49651

  3. Mesh or Prosthesis Implantation

    • The implantation of mesh or prosthetics during hernia repair is included in the main repair code.

Considerations for Coding

  • Conversion Procedures: Only report the successful technique if a procedure converts from laparoscopic to open surgery.

  • Imaging Guidance: When biopsies or drain placements are performed with imaging guidance, be sure to report the guidance code separately if applicable.

  • Complex Procedures: For complex procedures like liver or pancreatic transplants, report each part of the process separately.