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    v1.0.30
    OpenPayerBilling CodesOther Procedures on the AnusCPT cpt-46999-unlisted-procedure-anal-operations
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    CPT 46999: Unlisted Procedure, Anus

    CPT code 46999 is an unlisted procedure code used to report procedures of the anus that do not have a specific CPT descriptor; it is intended for surgical or diagnostic interventions on the anus and is typically reported for services provided in an ambulatory surgical center, hospital outpatient department, or inpatient surgical setting where the exact procedure performed lacks its own CPT code.

    For related coverage guidance, see recent payer policy updates: Percutaneous Electrical Nerve Field Stimulation for Functional Abdominal Pain Disorders, Esophagogastroduodenoscopy (EGD) Coverage Policy, Radiofrequency Therapy for Fecal Incontinence.

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    Table of contents

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    Clinical & Coding Specifications

    Clinical Context

    A 54-year-old patient presents to a colorectal surgery clinic with persistent anorectal symptoms after prior conservative treatment. The surgeon performs a procedure on the anus that does not match an established CPT descriptor — for example, an uncommon excision of an unusual perianal lesion, a novel local flap to repair an atypical anal defect, or a rare intraoperative maneuver to manage an anatomic variant. The workflow includes preoperative evaluation (history, focused anorectal exam, possible anoscopy), informed consent describing the unlisted nature of the procedure, intraoperative documentation detailing the indication, operative technique, time, and distinct steps, and submission of an operative report with supporting pathology or imaging as applicable for payer review. Typical site of service is an outpatient surgical center or hospital operating room. The service type is operative/anorectal surgery under the general category of anorectal procedures for conditions such as atypical masses, complex fissure/fistula variants, or reconstructive needs that lack a specific CPT code.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    46920Excision of perianal cyst, fistula, or abscess; simpleMay be performed for straightforward perianal disease that has specific coding; distinguishes when an unlisted code is not required.
    46040Anoscopy; diagnostic, with or without collection of specimen(s) by brush or forcepsCommon diagnostic adjunct performed before or after an unlisted anorectal procedure to assess mucosa and guide treatment.
    46221Hemorrhoidectomy, internal and external, single or multiple, with or without mucocutaneous (skin) bridge; simple, 1st or 2nd degreeOften considered when anorectal pathology involves hemorrhoidal disease; helps define when a specific code exists versus use of an unlisted code.
    46255Destruction of hemorrhoids, any method, 4 or more columns or pilesAlternative therapy for hemorrhoidal disease; may be performed alongside diagnostic or adjunct procedures.
    45330Sigmoidoscopy, flexible; diagnostic, with or without collection of specimen(s) by brushing or washingPerformed when broader lower GI evaluation is needed in the same setting or episode of care.

    Related Modifiers

    13 rows

    ModifierDescriptionWhen to Use
    22Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
    26Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
    50Modifier –50 (Bilateral Procedure) is appended to a CPT code when an identical procedure is performed on paired anatomical structures during the same operative session. The AMA states to add…- Use modifier -50 when the same CPT surgical, diagnostic, or radiology procedure is performed on paired anatomical structures (both sides of the body) during the same operative/session by the same…
    51Modifier –51 (Multiple Procedures) is used when the same provider performs multiple procedures in the same session to identify secondary, non‑exempt procedures and indicate payment reduction logic…- Use modifier -51 when the same provider performs multiple distinct procedures during the same patient encounter: report the highest‑valued procedure first (no modifier) and append -51 to…
    52Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
    53Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…
    58Modifier 58 (Staged or related procedure/service by the same physician during the postoperative period) indicates that a subsequent procedure performed by the same provider during the…- Use modifier 58 when the same physician/QHP performs a procedure during the postoperative/global period of an earlier procedure and the subsequent procedure is either planned or anticipated…
    59Modifier 59 indicates a distinct procedural service when two procedures that are not normally billed together are clinically and procedurally separate. The CPT definition (as reiterated by CMS)…- Use modifier -59 to report a distinct procedural service when documentation supports that the procedure reported is not normally billed together with another service on the same day because of a…
    62Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…
    78CPT modifier -78 indicates an unplanned, related return to the operating or procedure room by the same provider during the global postoperative period. It is appended when treatment for a…- Use modifier -78 when an unplanned, related complication during the original procedure’s global postoperative period requires the patient to return to a formal operating or procedure room and the…

    Showing 1–10 of 13

    Related Provider Taxonomies

    8 rows

    Taxonomy Code
    207T00000X
    208800000X
    2080P0201X
    261QM1100X
    2084P0005X
    363LC1500X
    173000000X
    2084P0301X

    Related ICD-10-CM Codes

    22 rows

    ICD-10-CM CodeDescription
    K57.20Diverticulitis of large intestine with perforation and abscess without bleeding
    K57.30Diverticulosis of large intestine without perforation or abscess without bleeding
    K57.90Diverticulosis of intestine, part unspecified, without perforation or abscess without bleeding
    K60.0Acute anal fissure
    K60.1Chronic anal fissure
    K60.2Anal fissure, unspecified
    K61.0Anal abscess
    K61.1Rectal abscess
    K62.5Hemorrhage of anus and rectum
    K62.6Ulcer of anus and rectum

    Showing 1–10 of 22

    Related Payer Policy Updates

    Specialty: Gastroenterology1 / 3

    10 rows

    PolicyPayerEffective Date
    Percutaneous Electrical Nerve Field Stimulation for Functional Abdominal Pain Disordersbcbsvermont2026-12-01
    Esophagogastroduodenoscopy (EGD) Coverage Policyevicore2026-11-05
    Radiofrequency Therapy for Fecal IncontinenceCigna2026-10-15
    Magnetic Sphincter Augmentation for the Treatment of Gastroesophageal Reflux Disease (GERD)univerahealthcare2026-10-15
    High-Resolution Anoscopy (HRA)Premera Bluecross2026-10-01
    Gastroesophageal and Gastrointestinal (GI) Services and ProceduresColorado Rocky Mountain Health Plans2026-10-01
    Fecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant TestingOscar Health2026-10-01
    Serum Testing for Hepatic Fibrosis in the Evaluation and Monitoring of Chronic Liver DiseaseOscar Health2026-10-01
    Pancreatic Enzyme Testing for Acute PancreatitisOscar Health2026-10-01
    Helicobacter pylori TestingOscar Health2026-10-01

    Frequently Asked Questions

    References

    1. 1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
    2. 2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
    3. 3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.
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