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    v1.0.30
    OpenPayerBilling CodesOther Procedures on the Colon and RectumCPT cpt-45999-unlisted-rectal-procedure
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    CPT 45999: Unlisted Procedure on Rectum

    CPT code 45999 is an unlisted procedure code used to report a rectal procedure without a specific CPT code when the service involves diagnostic or therapeutic intervention on the rectum; typical service type is surgical or procedural management of rectal pathology and the typical site of service is an ambulatory surgery center, hospital outpatient department, or operating room depending on clinical setting and complexity.

    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 patient presents with rectal pathology requiring a procedure that does not map to a specific CPT code — for example, an unusual excision or reconstruction of the rectum for a rare tumor, complex revision of a prior rectal repair, or an atypical transanal approach for removal of an intraluminal mass. Typical workflow: outpatient or ambulatory surgery center evaluation with history and focused rectal exam, endoscopic assessment (flexible sigmoidoscopy or rigid proctoscopy) to localize lesion, preoperative imaging as indicated (pelvic MRI or CT), informed consent describing off‑label or unlisted procedure reporting using 45999, operative documentation detailing indication, extent of dissection, technique, anesthesia type, intraoperative findings, and time. Postoperative care includes immediate recovery in PACU, pain management, wound and bowel function monitoring, and scheduled follow up for pathology review and wound check. Typical site of service: outpatient surgical center or hospital operating room. Typical service type: unlisted/complex rectal surgical procedure requiring physician operative report to support 45999 billing. Typical patient scenario: adult with symptomatic rectal lesion not removable by standard transanal polypectomy and not described by existing CPT codes, undergoing operative excision with partial rectal wall reconstruction under general anesthesia, requiring separate billing for anesthesia, professional component, and possible technical component for facility resources.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    45113Proctectomy, partial; with anastomosisPerformed for partial rectal resection when a specific resection code applies; may be an alternative to an unlisted rectal procedure when appropriate.
    45330Sigmoidoscopy, flexible; diagnostic, including collection of specimen(s) by brushing or washing, when performed (separate procedure)Preoperative diagnostic endoscopy to evaluate lesion prior to unlisted rectal surgery.
    45385Colonoscopy, flexible; with removal of tumor(s), polyp(s), or other lesion(s) by snare techniqueEndoscopic removal when lesion is amenable; if not feasible, leads to operative unlisted procedure reported with 45999.
    43499Unlisted procedure, esophagus; (placeholder for other unlisted GI procedures)Conceptually similar unlisted reporting for GI procedures when specific codes do not exist; shows parallel billing approach.
    99152Moderate sedation services provided by the same physician performing the diagnostic or therapeutic service (initial 15-30 minutes)May be billed when conscious sedation is provided for the rectal procedure and billing rules permit separate reporting.
    76930Ultrasound, transrectalPerformed intraoperatively or preoperatively for localization or guidance when indicated; may be billed separately if documented.

    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…
    54Modifier ‑54 (“Surgical care only”) is appended to a CPT surgical procedure when the reporting surgeon performs the intraoperative (surgical) component but does not furnish the preoperative and/or…- Use modifier -54 when the reporting surgeon provided only the intraoperative (surgical) component of a procedure and preoperative and/or postoperative management has been or will be provided by…
    55Modifier –55 indicates the billing provider furnished only postoperative management for a procedure that has a global surgical period. According to AAPC, this modifier is appended to the same CPT…- Use modifier -55 when billing the same CPT surgical code that has a 10- or 90-day global period and you, as a provider other than the original surgeon, furnished ONLY postoperative management (no…
    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
    207P00000X
    208D00000X
    363L00000X
    207K00000X
    2472V0600X
    2084B0002X
    152WP0200X
    246ZN0300X

    Related ICD-10-CM Codes

    26 rows

    ICD-10-CM CodeDescription
    A06.9Amebiasis, unspecified
    C20Malignant neoplasm of rectum
    D01.0Carcinoma in situ of colon
    D12.6Benign neoplasm of colon, unspecified
    D13.5Benign neoplasm of extrahepatic bile ducts
    K52.9Noninfective gastroenteritis and colitis, unspecified
    K56.7Ileus, unspecified
    K57.20Diverticulitis of large intestine with perforation and abscess without bleeding
    K57.30Diverticulosis of large intestine without perforation or abscess without bleeding
    K57.40Diverticulitis of both small and large intestine with perforation and abscess without bleeding

    Showing 1–10 of 26

    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

    Related Codes

    CPT-45399-UNLISTED-PROCEDURE-ON-COLON

    CPT 45399: Unlisted Procedure on Colon

    CPT-45990-DIAGNOSTIC-ANORECTAL-EXAMINATION-UNDER-ANESTHESIA

    CPT 45990: Diagnostic Anorectal Examination Under Anesthesia

    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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