Digestive diseases drive over 22 million hospitalizations annually, according to the American College of Gastroenterology, translating directly to coding complexity for gastroenterology practices. What seems like straightforward procedures often involve intricate anatomic variations, landmines, and stricter documentation requirements under the 2026 CMS guidelines.
NCCI bundling edits continue expanding, prior authorization requirements are becoming more strict, and payers are scrutinizing medical necessity more aggressively. In such a case, a thorough understanding of billing codes for gastroenterology prevents revenue leakage and keeps claims processing smooth. This guide breaks down the 13 most frequently reported gastroenterology CPT codes, modifier applications, and billing strategies essential for accurate reimbursement.
Gastroenterology CPT Code for Diagnostic Procedures
CPT Code 43200 – Esophagoscopy with specimen collection by brushing
This gastroscopy CPT code covers upper gastrointestinal examination using flexible endoscopy with brush cytology for specimen collection. The typical session time for this procedure ranges from 15 to 30 minutes. Documentation must explicitly state that specimens were collected for pathologic analysis. Commonly performed for patients with dysphagia, suspected esophageal pathology, or abnormal imaging requiring tissue confirmation.
CPT Code 91010 – Esophageal motility study with interpretation
The 91010 CPT code refers to an upper gastrointestinal motility test. Gastroenterology specialists use this code to inform payers that they have used a manometer to assess muscle pressure and movement within a patient’s esophagus. This procedure typically requires 30 to 60 minutes to complete. Documentation requires specific pressure measurements, coordinate analysis, and clinical correlation supporting medical necessity.
CPT Code 91022 – Duodenal motility study
This gastroenterology CPT code covers motility analysis of a patient’s stomach and duodenum. Gastroenterologists billing specialists use code 91022 to specify that a provider performed stomach and duodenal muscle pressure testing using a manometer. The session time for this examination typically ranges from 60 to 90 minutes. Used for patients with chronic nausea, vomiting, or suspected gastroparesis.
CPT Code 91034 – Gastroesophageal reflux test with nasal catheter pH electrode
The 91034 CPT code points toward a gastroesophageal reflux test performed over 24 hours. Billing experts use it to notify payers that a gastroenterologist assessed acid reflux using continuous pH monitoring via a nasal catheter. According to NCCI, effective 2022, CPT code 91034 bundles with 91038 when performed simultaneously, creating a common denial trigger.
CPT Code 91035 – Gastroesophageal reflux test with wireless telemetry pH electrode
CPT code 91035 is similar to 91034 but specifies pH monitoring via wireless telemetry electrodes instead of a nasal catheter. The 91035 gastroenterology CPT code indicates that doctors evaluated gastroesophageal reflux disease severity by temporarily attaching a pH probe to the esophageal mucosa. This wireless device transmits data and offers superior patient tolerance with extended monitoring periods lasting 48 to 96 hours.
CPT Code 91040 – Esophageal balloon distension study
The 91040 CPT code covers an esophageal balloon distension study used to evaluate lower esophageal sphincter response. Gastroenterology doctors use this code for non-cardiac chest pain workups. During this procedure, which typically takes 30 to 45 minutes, gastroenterologists insert a deflated balloon into the lower esophageal sphincter, then gradually fill it to stretch muscle fibers.
CPT Code 91065 – Breath hydrogen/methane test
The 91065 CPT code refers to a hydrogen or methane breath test. Billing specialists use this code to claim reimbursement for diagnosing gastric functionality problems, including SIBO, lactose intolerance, and fructose malabsorption. This non-invasive test requires 120 to 180 minutes to complete and is conducted after 8-12 hours of fasting with proper medication restrictions.
CPT Code 91200 – Liver elastography
The 91200 code is one of the most commonly used CPT codes for gastroenterology. It refers to liver elastography performed to determine liver stiffness using FibroScan technology. This test helps gastroenterology specialists assess fibrosis and distinguish between benign and malignant liver pathology. The procedure session typically lasts 10 to 15 minutes. Documentation requires stiffness measurements in kilopascals, technical success rate, and interquartile range values.
CPT Code 91133 – Electrogastrography
This CPT code for gastroenterology refers to diagnostic transcutaneous electrogastrography. Billing specialists use the 91133 code to claim reimbursement for checking stomach muscle function. During this procedure, which takes 60 to 120 minutes to complete, gastroenterology doctors place electrodes over the patient’s abdomen to measure electrical potential and gastric myoelectrical activity.
Gastroenterology CPT Code for Imaging Procedures
CPT Code 91110 – Capsule endoscopy, esophagus through ileum
Billing specialists use the 91110 CPT code to bill capsule endoscopy procedures for analyzing a patient’s digestive system. During this process, the doctor instructs patients to swallow a pill-sized capsule containing a camera that takes pictures of their gastrointestinal tract from the esophagus to the ileum. The complete transit time through the small bowel typically ranges from 8 to 12 hours. This non-invasive method examines hard-to-reach areas that traditional endoscopy cannot visualize. Medicare Part B shows 9% year-over-year utilization increase in this CPT code for endoscopy.
CPT Code 91122 – Anorectal manometry
Gastroenterology doctors use the 91122 CPT code to notify payers that they analyzed and measured a patient’s rectum and anal sphincter contraction. This test explores reasons for fecal incontinence, constipation, and bowel movement issues. The procedure session typically requires 30 to 60 minutes. Documentation must include pressure measurements, reflex testing, and clinical correlation.
Gastroenterology CPT Code for Therapeutic Procedures
CPT Code 43215 – Esophagoscopy with foreign body removal
This gastroenterology CPT code highlights an esophagoscopy procedure with therapeutic intervention. Billing specialists use this code when gastroenterology doctors use a flexible esophagoscope to unblock the esophagus and remove foreign bodies, usually large food pieces or accidentally swallowed objects. The procedure typically takes 20 to 45 minutes to complete. Documentation requires foreign body type, anatomic location, and removal technique specification.
CPT Code 43216 – Esophagoscopy with tumor/polyp removal by hot biopsy forceps
The 43216 gastroenterology CPT code specifies an esophagoscopy to remove abnormal growths using electrocautery. Gastroenterology specialists use this code to inform insurance companies that they used a flexible tube with a camera to look inside the patient’s esophagus and remove abnormal masses via hot biopsy forceps. This therapeutic intervention typically requires 30 to 60 minutes. Following the procedure, specialists send resected specimens to laboratory specialists for histopathologic analysis.
Gastroenterology CPT Code Comparisons
| CPT Codes | Primary Difference | Key Considerations |
| 91034 vs. 91035 | Both measure gastroesophageal reflux through pH monitoring | 91034: Nasal catheter electrode, 24-hour monitoring 91035: Wireless telemetry capsule, 48–96-hour monitoring, superior patient tolerance |
| 43200 vs. 43215 vs. 43216 | All involve flexible esophagoscopy with varying complexity levels | 43200: Diagnostic examination only with specimen collection 43215: Adds therapeutic foreign body removal 43216: Includes tumor/polyp resection via electrocautery with histopathology |
| 91110 vs. 91111 | Capsule endoscopy with different anatomic coverage | 91110: Esophagus through ileum (small bowel focus) 91111: Extends through colon, requires bowel preparation and extended monitoring |
Conclusion
The difference between clean gastroenterology claims and denials comes down to three factors: knowing which CPT code matches the procedure performed, documenting clinical reasoning that justifies medical necessity, and catching NCCI bundling issues before claims leave your practice.
These 13 gastroenterology CPT codes represent the backbone of GI billing, but accurate code selection is only half the battle. Payers increasingly demand proof that diagnostic testing was medically necessary based on failed conservative management, not simply clinically convenient.
Gastroenterology billing shouldn’t be a constant battle with denials and underpayments. Nexus io specializes in gastroenterology billing services, combining certified coder expertise with deep CMS guideline knowledge and current NCCI edit awareness.
We track quarterly bundling updates, monitor payer policy changes, and handle appeals so your practice collects every dollar earned.
Frequently Asked Questions
Q: When is modifier 26 required for gastroenterology procedures?
A: When physicians interpret diagnostic tests and do not own the equipment used in the test, the modifier 26 applies. For example, hospital-based practices may use modifiers because these facilities will have the FibroScan equipment, and the physician on staff analyzes the data.
Q: Can CPT codes 91034 and 91035 be billed together?
A: According to CPT, codes 91034 and 91035 cannot be billed together because they are different methods of accomplishing the same diagnostic goal. It will be necessary to choose which method was used in monitoring, whether it was the nasal catheter (91034) or the capsule via wireless technology (91035).
Q: What documentation supports medical necessity for CPT 91200 liver elastography?
A: Medical necessity requires documenting the presence of chronic liver disease or a chronic hepatic condition, the presence of elevated aminotransferase levels, the presence of a fatty liver via imaging, or Metabolic Syndrome. In addition, a series of liver elastography studies would provide evidence of either disease progression or response to treatment.
Q: Does Medicare cover CPT 91110 capsule endoscopy without prior authorization?
A: Currently, the majority of Medicare Administrative Contractors require prior authorization for CPT 91110. The contractor needs to be able to demonstrate that traditional endoscopy was unsuccessful in finding the bleeding location. Therefore, it is important to verify the coverage criteria for CPT 91110 with the appropriate contractor before scheduling to help reduce denials.
Q: Can diagnostic and therapeutic gastroenterology procedures be billed on the same day?
A: Yes, when procedures are distinct and require separate medical necessity evidence. Modifier 59 should only be used when operations are performed at various anatomic sites or when they represent independent services that are not subject to NCCI bundling.
