Gastroenterology billing stands apart from most specialties because the gastrointestinal tract spans multiple organs, each carrying its own CPT code families, modifier rules, documentation thresholds, and payer-specific requirements. For example, when billing for an esophageal motility study, you must make component billing decisions, consider NCCI bundling risks when billing for pH monitoring and endoscopy codes, and meet the shifting requirements for medical necessity under the requirements of Medicare, Medicaid, and commercial carriers.
That complexity is exactly why the billing team at Nexus io created this guide to break down one of the most commonly billed yet frequently denied gastroenterology procedure codes. This guide explains the official CPT descriptor for code 91010, clinical scenarios that validate the study with ICD-10-CM links, all modifiers applicable, including those in the CMS subset that so many other guides do not cover, NCCI bundling edits that result in most claim denials, and what documentation and reimbursement standards will be in effect in 2026.
If your practice bills esophageal manometry and you want to stop leaving revenue on the table, this guide covers what you need to know.
CPT Code 91010 – Description
CPT code 91010 falls within the “Upper Gastrointestinal Motility Studies” range, maintained by the American Medical Association (AMA). The code encompasses both the professional and technical components of esophageal manometry.
During the procedure, the physician advances a pressure-sensing catheter through the nose into the esophagus and gastroesophageal junction (GEJ) to assess esophageal muscle movement. The physician will then be able to use HRM metrics recorded throughout the study to interpret the findings according to the CCv4.0, including IRP, DCI, and DL. A written report will be completed by the physician to finalize the findings.
Scenarios Where CPT Code 91010 is Applicable
GERD Evaluation with Refractory Symptoms
Patient reports constant burning sensation in the retrosternal area (heartburn), experience of acidic fluid in throat (regurgitation), and sharp pain just behind the sternum (retrosternal pain) despite appropriate PPI therapy. Manometric evaluation provides data about the lower esophageal sphincter (LES) competence (i.e., functioning) and peristaltic function to determine surgical candidacy for fundoplication.
Results of the study demonstrate decreased resting LES pressure and ineffective esophageal motility (IEM). Code report as 91010 with ICD-10-CM codes K21.0 (GERD with esophagitis) or K21.9 (GERD without esophagitis).
Confirming Achalasia
A patient with progressive dysphagia to solids and liquids after endoscopy excludes mucosal pathology. HRM demonstrates absent peristalsis with elevated IRP, consistent with Type I achalasia under CCv4.0. Report with K22.0 (achalasia of cardia). After diagnosis has been established, treatment can be determined based upon the diagnosis given: either pneumatic dilation, Heller myotomy, or per-orifice endoscopic myotomy (POEM).
Pre-Operative and Post-Fundoplication Assessment
For any type of Nissen, Toupet, or Dor fundoplication procedure, performing manometry is required prior to determining if the patient has sufficient peristaltic reserve. This helps to rule out achalasia as a contraindication that would prevent performing a full 360-degree fundoplication wrap on the patient.
Post-operatively, manometric evaluation can be helpful in establishing the cause of recurrence of dysphagia, either related to wrap failure or dysmotility following surgery. This assessment would be coded either R13.10 (dysphagia, unspecified) or R13.19 (other dysphagia).
Cardiac Chest Pain
After a cardiac evaluation demonstrates that chest pain is not due to ischemia, manometric examination will reveal disorders affecting motility within the esophagus; including distal esophageal spasm (DES: defined as having 20% or greater premature contractions with a DCI greater than 450 mm Hg·s·cm based upon CCv4.0), jackhammer esophagus (defined as hyper-contracted with a DCI in excess of 8000 mm Hg·s·cm), and lack of contractability. This assessment will be coded using R07.89 (other chest pain) or K22.4 (dyskinesia of esophagus).
Applicable Modifiers for CPT Code 91010
Modifier 26
This modifier bills the professional component only: physician interpretation and written report.
Modifier TC
Modifier TC bills the technical component. It includes procedure execution, catheter, manometry equipment, and staff. No other modifier is required when a single entity performs and interprets the study globally.
Modifier 52
This modifier reports a study reduced in scope (fewer swallows than the CCv4.0 protocol defines).
Modifier 53
It is for reporting a study that was initiated but discontinued due to patient distress or clinical risk.
Modifier 76
This modifier indicates same-physician same-day repeat; Modifier 77 indicates different-physician same-day repeat.
Modifier 59
The NCCI bundling edit for 91010 is now an exception when the procedure is considered different than the same-day pH monitoring or endoscopy. The Centers for Medicare & Medicaid Services (CMS) prefers the specificity of modifiers: XE (separate encounter), XS (separate structure), XP (separate practitioner), and XU (unusual non-overlapping service); instead of 59, which may subject the provider to additional scrutiny for audit purposes.
By using XE or XS, the modifier usage will have less likelihood of triggering additional audits and will provide a concise and well-supported clinical rationale for services billed. Any organization exhibiting consistent modifier errors in its gastroenterology billing should prioritize a more in-depth training of their coders regarding these modifier distinctions.
NCCI Bundling Edits and Denial Triggers
NCCI procedure-to-procedure (PTP) edits generate the majority of 91010 denials, and most billing guides omit this entirely.
91010 vs. 91013
CPT code 91013 (esophageal motility study utilizing perfusion or stimulation) is considered an add-on code to 91010. When stimulation occurs, 91013 must be billed in conjunction with 91010 and may not be additionally billed as a standalone because the base study is included. Billing 91013 as a standalone code without 91010 will cause an automatic denial.
91010 vs. pH monitoring codes
When submitting codes 91034 (nasal catheter pH electrode), 91035 (Bravo capsule), 91037 (impedance with nasal catheter), and 91038 (impedance with mucosal electrode), the same day as 91010, an appropriate documentation of a clinical necessity for the submission of an additional code using modifier 59 or XE/XS must be contained in the records.
Note: NCCI edits have been applied since January 2022 to 91038 to bundle with the submission of 91034. The documentation and billing for the same-date submission of any of the three will require diligent documentation and adjustment/billing of a modifier.
91010 vs. endoscopy codes
The same guidelines apply when submitting 91010 with EGD code submissions (i.e., 43235, 43239, 43249) on the same date of service, and appropriate documentation must be present in the medical record indicating a medical necessity for submitting each procedure using modifier 59 or XS is necessary.
Medically Unlikely Edits (MUE)
The MUE for 91010 is one unit per provider per date of service. A provider submitting for greater than 1 unit for 91010 would cause an automatic denial regardless of the modifier used.
CPT Code 91010 – Billing and Reimbursement Guidelines
Establish Medical Necessity
Clinical indication must be provided. Diagnoses of GERD being treatment resistant, Achalasia suspected, checking motility prior to Fundoplication, and unexplained dysphagia after all structural defects have failed to explain. The ICD-10-CM codes available to show medical need include: K21.0/K21.9 (GERD), K22.0 (Achalasia), K22.4 (DES), R13.10-19 (Dysphagia), and R07.89 (Chest Pain). Some payers also accept K20.0 and K20.9 if being run as part of the EoE workup; however, it is best to verify that your MAC posts a Local Coverage Determination (LCD) that would allow you to bill these.
Ensure Comprehensive Documentation
You will have to document the type of catheter used, which position the patient was in at the time of the cath; which swallows were done according to the swallow protocol, and whether there were complications with the procedure. You must include, but may not be limited to, LES pressure, IRP, DCI, distal latency, Peristaltic classification, and an overall impression of testing according to the Chicago Classification 4.0 – all tests must be interpreted completely, or there will be post-payment audit clawbacks on motility testing.
Payer-Specific Policies
Medicare coverage varies by MAC jurisdiction. The CY 2026 PFS conversion factor is $33.40 (non-qualifying APM, +3.26% over 2025) with a finalized negative 2.5% efficiency adjustment on certain diagnostic valuations. The rate of prior authorization for commercial payers like UnitedHealthcare, Aetna, Cigna, and BCBS is typically required, and some will require a prior endoscopy before allowing payment for a manometry study. Timely filing limits will fall between 90 days for commercial and 12 months for Medicare. Practices weighing whether to manage billing in-house or outsource should factor in this complexity.
Summary
This guide covered CPT 91010 under the CCv4.0 framework, four clinical scenarios with ICD-10-CM linkages (K21.0, K21.9, K22.0, K22.4, R13.10–R13.19, R07.89), seven modifiers plus CMS subset modifiers XE through XU, NCCI PTP edits between 91010 and codes 91013, 91034, 91035, 91037, and 91038, MUE thresholds, and 2026 Medicare and commercial payer reimbursement guidelines.
When every 91010 claim requires correct component splitting, CCv4.0-compliant documentation, NCCI edit navigation across five related procedure codes, and payer-specific LCD verification, the margin for coding error is nearly zero. Achieving that type of accuracy with a general billing staff cannot be done consistently. Nexus io focuses solely on the complexities of gastroenterology billing using AAPC-certified coders who specialize in motility study documentation and artificial intelligence to scrub a claim on the front end for any bundling conflicts or modifier errors prior to submission.
As a result, their entire clientele has experienced a first pass clean claim rate of 98%, a collection ratio of 97%, 30% reduction in AR days, and an average of 30% revenue growth in the first several months of their relationship. Talk to the experts at Nexus io to see how their gastroenterology billing services handle the codes your practice bills most.
Frequently Asked Questions
What is the difference between CPT 91010 and 91013?Â
CPT Code 91010 represents the basic study of esophageal manometry, while CPT code 91013 is only used in conjunction with code 91010 when any type of stimulation or perfusion (acid, alkali, or IV medication) occurs during the procedure.Â
Does CPT code 91010 require a modifier?Â
No, not if you have billed for the service as the global provider. You must use either modifier 26 or TC if you have split the professional and technical components between different providers. There are certain modifiers (52, 53, 59, 76, 77, XE, XS, XP, XU) that can be used depending on the specific situation.
Is CPT 91010 a surgical procedure?Â
No, the code is considered a diagnostic procedure and has an indicator of XXX in the Medicare Physician Fee Schedule, which means that it does not have a global surgery period.
Can 91010 be billed the same day as upper endoscopy?Â
Yes, as long as you have attached either modifier 59 or XS to 91010 and have documented that the esophageal manometry (91010) and upper endoscopy (43235, etc.) were for different clinical indications.
