CPT code 88262 – Chromosome analysis, 15-20 cells with 2 karyotypes

Key takeaways

CPT code 88262 covers chromosome analysis with banding: A count of 15-20 cells and 2 karyotypes. Tissue culture (88230-88239) and interpretation (88291) are billed separately.

Cell count and karyotype count both define the code. 88261 is 5 cells with 1 karyotype, 88263 is 45 cells for mosaicism with 2 karyotypes, and 88264 analyzes 20-25 cells.

Amniotic fluid and chorionic villus samples are coded 88267 or 88269, not 88262, with culture under 88235.

Medicare covers 88262 when the test meets the applicable MAC LCD criteria. Most commercial payers require prior authorization.

Pabau’s claims management software supports clean-claim submission and denial tracking for cytogenetics laboratory billing.

CPT code 88262: Official descriptor and procedure overview

CPT code 88262 is defined by the American Medical Association (AMA) as: “Chromosome analysis; count 15-20 cells, 2 karyotypes, with banding.” The code sits within the 88230-88299 Cytogenetic studies subsection of the Pathology and Laboratory chapter.

The service covers harvest and slide preparation, G-banding (or an equivalent banding technique), a chromosome count of 15 to 20 cells, and two karyotypes. Tissue culture is billed separately under 88230-88239. Physician interpretation and the written report are billed under CPT 88291.

The code applies to peripheral blood, bone marrow aspirate, and solid tissue specimens. What matters is that 15 to 20 metaphase cells are counted and two karyotypes prepared. Prenatal specimens are coded differently. Amniotic fluid and chorionic villus studies use 88267 or 88269, and their culture is reported under 88235.

What CPT 88262 covers and excludes

Understanding the boundaries of 88262 prevents both under-billing and bundling errors. The table below summarizes what is included in the service and what must be coded separately.

Because culture and interpretation sit outside 88262, one karyotype study often reaches the payer as three codes. The map below shows which code covers each stage.

88261 vs 88262 vs 88263 vs 88264: Choosing the right code

The chromosome analysis family (88261-88264) splits on two variables: How many cells are counted or analyzed, and how many karyotypes are produced. Coding on cell count alone is how 88262 claims get miscoded, so check both numbers in the cytogenetics report.

Verify the cell count and the karyotype count in the cytogenetics laboratory report before you select a code. A report of 14 cells does not support 88262, and neither does a report with one karyotype. If the report documents 22 cells, 88264 is the code to check. The report is the audit trail.

Common clinical indications for CPT 88262

Medical necessity is the gatekeeper for every CPT 88262 claim. The ordering physician’s documentation must establish a clinical indication that justifies chromosome analysis at the 15-to-20-cell level. Labs billing 88262 for fertility workups should confirm that the ordering clinician’s note links the test to a specific diagnosis or diagnostic question.

• Male infertility: Karyotyping identifies chromosomal causes such as Klinefelter syndrome (47,XXY) or structural rearrangements linked to azoospermia or oligospermia.
• Recurrent pregnancy loss: Parental karyotypes are ordered to detect balanced translocations or inversions that may cause repeated miscarriage. The diagnosis to link is usually N96.
• Congenital anomaly evaluation: Newborns with dysmorphic features, cardiac defects, or multiple anomalies undergo karyotyping to identify trisomies, deletions, or duplications.
• Prenatal diagnosis: Amniotic fluid or chorionic villus samples taken after abnormal screening or ultrasound findings are not coded 88262. They are coded 88267 or 88269, with culture under 88235.
• Hematologic malignancy staging: Bone marrow chromosome analysis at diagnosis or relapse of leukemia, myelodysplastic syndrome, or lymphoma supports treatment planning.
• Developmental delay or intellectual disability: Chromosomal imbalance is a common underlying cause investigated through karyotyping when microarray results are inconclusive.

Accepted ICD-10 codes to bill with CPT 88262

Diagnosis code selection determines whether the claim clears the payer’s medical-necessity edits. The table below lists high-use ICD-10-CM codes accepted with CPT 88262. Some Medicare Administrative Contractors (MACs) publish Local Coverage Determinations (LCDs) with their own covered diagnosis lists. Check the applicable MAC LCD before billing.

Medicare and payer reimbursement rates for CPT 88262

Chromosome analysis is a laboratory test. CPT 88262 is therefore priced under the Medicare Clinical Laboratory Fee Schedule (CLFS) rather than the Physician Fee Schedule (MPFS).

Check the current-year rate in the CLFS files at cms.gov before you quote a figure.

Prior authorization requirements for chromosome analysis

Medicare generally does not require prior authorization for medically necessary laboratory tests including CPT 88262, provided the applicable MAC LCD’s coverage criteria are met. Commercial payers are a different story. Understanding medical billing fundamentals for genetic testing helps billing staff anticipate which payer classes will gate this test.

• Large commercial plans (UnitedHealthcare, Aetna, Cigna, Anthem): Prior authorization is commonly required for elective cytogenetic testing.
• Medicaid managed care: Requirements vary by state and managed care organization. Some plans follow Medicare LCD criteria, while others set their own.
• Medicare Advantage: Plans may add prior authorization requirements that traditional Medicare does not impose. Verify with the specific plan before ordering.
• Self-insured employer plans: Requirements vary widely, so review the plan document or contact the third-party administrator (TPA).

A prior authorization request should include the ordering physician’s clinical note and the specific ICD-10 code. Add any prior test results, such as an abnormal ultrasound, an inconclusive microarray, or a semen analysis. Standard requests typically take three to five business days. Urgent requests may qualify for a payer’s expedited review.

How to document CPT 88262 for billing compliance

A clean chromosome analysis claim depends on documentation that travels from the ordering physician’s office to the laboratory, then to the payer. Following billing compliance requirements specific to cytogenetics reduces audit exposure and speeds payment.

1. Ordering physician order: A signed order stating the diagnosis or clinical question, the specimen source, and the test ordered. For 88262, that is chromosome analysis counting 15-20 cells, with 2 karyotypes and banding. Verbal orders must be co-signed within the timeframe required by the payer or applicable regulations.
2. Specimen documentation: Record the specimen type (peripheral blood, bone marrow, or solid tissue), collection date, and handling conditions. Amniotic fluid is coded 88267 or 88269 instead. Payer LCDs often specify accepted specimen types for particular indications.
3. Cytogenetics laboratory report: The report must state the exact number of cells counted (15-20) and the banding technique used. It also records the two karyotypes, their result, and the date of analysis. This is the primary clinical record supporting the CPT 88262 selection.
4. Karyotype image retention: Keep digital or photographic karyotype images for the period CAP and CLIA standards require. Payers may request them during an audit.

Modifiers and bundling rules for CPT 88262

Modifier errors on cytogenetics claims trigger NCCI bundling denials that need corrected claims. A clean claim for 88262 carries modifier 59 or an X{EPSU} modifier only when another chromosome analysis code covers a distinct specimen.

NCCI bundling edits pair 88262 with 88261, 88263, and 88264 as potentially mutually exclusive on the same date for the same specimen. When two of them are legitimately billed, modifier 59 (or an XE/XS/XP/XU modifier) may be required. Documentation must show each is a distinct service on a distinct specimen or indication.

Top reasons CPT 88262 claims are denied

Denial patterns on chromosome analysis claims cluster around three failure points: Documentation, diagnosis linkage, and administrative requirements. Effective denial management workflows address each of these proactively rather than after the denial hits.

See the full list of common denial codes for the remittance codes that accompany these denials.

• Non-covered or missing ICD-10 code: The diagnosis code is missing, or it is not on the payer’s covered list for cytogenetic testing. Fix: Review the MAC LCD or payer policy and confirm a covered ICD-10 code is linked to the claim before submission.
• Insufficient cell count documentation: The cytogenetics report omits the number of cells counted, or gives a number outside the 15-20 range for 88262. Fix: Require the laboratory to include the exact cell count in the final report before billing.
• Bundling and modifier errors: 88291 is billed without a signed interpretation and report. A second chromosome analysis code can also go out without modifier 59 for a distinct specimen. Fix: Attach the cytogeneticist’s report to every 88291 line, and document the separate specimen before adding 59.
• Prior authorization not obtained: A commercial payer required preauth and none was secured before specimen collection. Fix: Implement a preauth check at the point of order entry, not at billing.
• LCD policy non-compliance: The clinical indication does not meet the MAC LCD criteria for the diagnosis submitted. A routine wellness karyotype with no clinical indication is the classic example. Fix: Verify LCD criteria before ordering, and document the specific clinical question in the ordering note.
• Incorrect place-of-service code: POS code does not match the setting where the laboratory work was performed. Fix: Use POS 81 (independent laboratory) for reference labs and POS 22 (outpatient hospital) for hospital-based labs.

Can CPT 88262 be billed with 88291?

Yes, CPT 88262 and 88291 can be billed together on the same date. CPT 88262 is the laboratory analysis, which covers harvest, banding, imaging, the cell count, and the two karyotypes. Tissue culture is reported separately under 88230-88239.

CPT 88291 is the cytogeneticist’s interpretation and written report. It is a professional-only code, so there is no TC/26 split on either line. Before you submit the pair, confirm the signed report is on file to support 88291.

How Pabau keeps 88262 claims moving

A clean 88262 claim rests on four checks: The cell count, the karyotype count, the preauth status, and 88291 billed alongside the analysis. When billing staff run those checks by hand after the report arrives, a single miss sends the claim back.

Pabau sends electronic claims through its Claim.MD integration to thousands of US payers. Eligibility checks can flag whether a patient’s plan covers cytogenetic testing before the specimen is sent.

Pabau’s claims management software tracks the required documentation fields before submission. Missing items surface on your side, before they trigger a denial or a records request.

Streamline your cytogenetics billing workflow

Pabau connects with Claim.MD to submit lab claims to thousands of US payers and check eligibility. It also tracks denials across the cytogenetics code family.

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Conclusion

CPT 88262 holds up only when the report proves two numbers: 15 to 20 cells counted and two karyotypes produced. Treat those figures as the coding decision, and the choice between 88261, 88263, and 88264 follows from them.

Settle the payer side before the specimen leaves the practice. That means preauth for commercial plans, a covered ICD-10 code tied to the ordering note, and 88291 reported with the analysis. Checks built into order entry leave far fewer claims to correct after a denial.

Book a demo to see how Pabau handles cytogenetics and laboratory billing from order to payment.

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