When coding for colonoscopies for Medicare patients it is crucial to understand the following:

  1. What is a screening colonoscopy?
  2. Which codes are applicable?
  3. Is a modifier required?

In some scenarios, it is also helpful to know what coverage limitations apply.  Let’s take a closer look!

Screening Colonoscopies

A screening colonoscopy is provided to a patient in the absence of signs or symptoms based on the patient’s age, gender, medical history, and family history and typically based on medical guidelines. The formal definition of “screening” describes a colonoscopy routinely performed on an asymptomatic person for the purpose of testing for cancer or colorectal polyps.

Now, it is not that uncommon for the surgeon to remove one or more polyps at the time of a screening colonoscopy, which would be a therapeutic procedure, even though the procedure  began as a screening.  Whether a polyp or cancer is ultimately found does not change the screening intent of that procedure.

Two Sets of Codes

The Centers for Medicare and Medicaid Services (CMS) developed the HCPCS codes to differentiate between screening and diagnostic colonoscopies in the Medicare population.  When choosing a CPT/HCPCS code, be sure to link the appropriate diagnosis code based on documentation.

Keep in mind that for screening colonoscopies, the screening diagnosis is always reported as primary.  If found, the polyp(s) is reported as a secondary diagnosis.  However, , the provider should not report the screening colonoscopy code for the CPT but rather the code for the diagnostic or therapeutic procedure performed.




Colonoscopy, flexible, diagnostic


Screening colonoscopy on individual at high risk


Screening colonoscopy on individual not meeting the criteria for high risk




Encounter for screening for malignant neoplasm of colon


Family history of malignant neoplasm of digestive organs


Personal history of colonic polyps

CMS defines ‘high risk’ as a patient with a:

  • close relative (sibling, parent, or child) who has had colorectal cancer or an adenomatous polyp
  • family history of familial adenomatous polyposis
  • family history of hereditary nonpolyposis colorectal cancer
  • personal history of adenomatous polyps
  • personal history of colorectal cancer
  • inflammatory bowel disease, including Crohn’s Disease, and ulcerative colitis

Modifier PT

CMS developed the PT modifier to indicate that a colonoscopy scheduled as a screening was converted to a diagnostic or therapeutic procedure.  The PT modifier (colorectal cancer screening test, converted to diagnostic test or other procedure) is appended to the CPT code.

For example, if a non-high-risk patient presented for a screening colonoscopy and the provider performed a polyp removal with hot biopsy forceps, you would report code 45384-PT with a primary diagnosis code of Z12.11 followed by the appropriate polyp diagnosis code (e.g., K63.5).

Some commercial payers follow CMS guidelines for the use of PT modifier, but some do not.  It is always good to check your payer guidelines before filing the claim to verify specific requirements.

Colorectal Cancer Screening Coverage

Several organizations have issued guidelines on colorectal rectal screening. While most guidelines recommend routine screening for adults starting at age 50, the frequency and screening age, as well as the preferred screening method can differ. If the patient is considered high-risk for colorectal cancer, this can also change screening guidelines.

Per CMS, screening colonoscopies are covered once every 120 months, or 48 months after a previous flexible sigmoidoscopy, and there is no minimum age requirement.  For high-risk patients, a colonoscopy is covered once every 24 months.  Although the screening is covered, if a polyp of other tissue is found and removed during the colonoscopy, the patient may still be responsible for 20% of the Medicare-approved amount for the physician services, and a copayment in the hospital setting.  Part B deductible doesn’t apply.

Check out these resources for more information:




Mary is a consultant for The Haugen Consulting Group with over 25 years of health care industry experience. She started her career in Orthopedics which was her passion for decades. In addition to Orthopedics, she provides expertise in other specialties such as Anesthesia, Ambulatory Surgery Center, as well as most surgical specialties . She has experience working the professional fee side of coding, audit, education as well as compliance, serving both coders and physicians, as well as the surgical side. She is a Certified Professional Coder (CPC), Certified Professional Medical Auditor (CPMA), Certified Anesthesia Professional Coder (CANPC) Certified Ambulatory Surgery Center Coder (CASCC) and Certified Orthopedic Surgery Coder (COSC).

During her free time, she loves to do crafts, enjoys the outdoors, and the Broncos! She has 4 daughters, and 10 grandchildren which light up her life.


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