Accurate gastroenterology coding is critical for reimbursement and compliance. This reference covers the most-used ICD-10-CM diagnosis codes and CPT procedure codes for gastroenterology practices in the United States. Whether you are billing for GERD management, colonoscopy, or IBD care, these codes reflect current CMS guidelines and are updated for the 2025-2026 fiscal year.
FY 2026 ICD-10-CM (CMS) · CPT codes updated annually · All codes verified billable · Last verified: June 2026
Colonoscopy, flexible, with removal of polyp by snare
~$270.40
-PT, -59
43239
Esophagogastroduodenoscopy (EGD) with biopsy
~$200.30
-59
43235
Esophagogastroduodenoscopy (EGD), diagnostic
~$165.20
-53
43200
Esophagoscopy, flexible; diagnostic
~$140.90
-53
45330
Sigmoidoscopy, flexible; diagnostic
~$115.70
-53
91110
GI tract imaging, intraluminal, capsule endoscopy
~$695.00
-26, -TC
74263
CT colonography, screening
~$85.40
-26, -TC
91034
Esophageal reflux test with nasal catheter pH electrode
~$65.30
-26, -TC
99213
Office outpatient visit, established patient, low complexity
~$77.50
-25, -95
99214
Office outpatient visit, established patient, moderate complexity
~$111.90
-25, -95
*Approximate 2025 CMS national non-facility rate. Rates vary by geography, setting, and payer contract. Refer to the CMS Physician Fee Schedule for official rates.
Top Denial Reasons for Gastroenterology Claims
⚠
Medical Necessity Not Documented
Diagnostic colonoscopy and EGD require documented symptoms, family history, or a failed conservative treatment trial supporting the clinical indication before the procedure is billed.
⚠
Missing or Incorrect Modifier
A screening colonoscopy (Z12.11) that becomes diagnostic due to a polypectomy or biopsy is frequently denied, or the patient is incorrectly balance-billed, when the -PT modifier is omitted on the CPT code.
⚠
Prior Authorization Not Obtained
Capsule endoscopy (91110) and certain advanced GI imaging studies often require prior authorization. Confirm payer-specific requirements before scheduling.
⚠
Diagnosis-Procedure Code Mismatch
Claims are denied when a biopsy or polypectomy code (45380, 45385) is billed without a supporting pathology or lesion diagnosis, or when a screening code is paired with a diagnostic-only CPT. Cross-check NCCI edits before submission.
Gastroenterology Billing & Coding Tips
Distinguish screening (Z12.11) from diagnostic colonoscopy — when a screening exam becomes diagnostic due to a polypectomy or biopsy, append modifier -PT so the patient retains ACA no-cost-share preventive benefits.
Document Crohn’s disease (K50.x) and ulcerative colitis (K51.x) with location and complication status for maximum diagnosis specificity.
45380 and 45385 are not separately billable with 45378 in the same session — the higher-value code supersedes per NCCI edits.
GERD (K21.9) alone rarely supports EGD medical necessity for payers — pair it with documented alarm symptoms or a failed PPI trial when applicable.
Use K21.9 for GERD without esophagitis, or K21.0 when esophagitis is documented. Always code to the highest specificity supported by the documentation.
What CPT code is used for a diagnostic colonoscopy?
45378 covers a diagnostic colonoscopy. If a biopsy is taken, use 45380 instead; if a polyp is removed by snare, use 45385.
Is a screening colonoscopy billed differently than a diagnostic one?
Yes. A screening exam is reported with Z12.11. If a polypectomy or biopsy is performed during that same screening, append modifier -PT to the CPT code so the patient keeps their no-cost-share preventive benefit.
How does OmniMD help with gastroenterology coding?
OmniMD’s EHR suggests ICD-10 and CPT codes directly in the encounter workflow, reducing manual lookup time and claim denial rates.
What is the difference between K50.90 and K51.90?
K50.90 is Crohn’s disease, unspecified, without complications. K51.90 is ulcerative colitis, unspecified, without complications. The two are distinct forms of inflammatory bowel disease and are not interchangeable.
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