Preimplantation Genetic Testing —
Biopsy, Analysis, and Transfer Billing
Short answer: a PGT cycle bills as two claims filed by two different entities — the fertility clinic bills the embryo biopsy (CPT 89290 or CPT 89291) as part of the underlying IVF cycle, and the reference genetics lab bills the chromosomal or molecular analysis (PGT-A, PGT-M, or PGT-SR) directly to the payer or the patient under a separate agreement. The embryos then transfer in a subsequent frozen embryo transfer cycle billed as its own episode. Getting these three claims — biopsy, analysis, and transfer — sequenced, authorized, and priced correctly is the entire billing problem.
What changes case to case is not the code set but the coverage track. PGT-A for advanced maternal age or recurrent pregnancy loss is often covered under a medical indication; PGT-M for a documented single-gene disorder is authorized case-by-case with genetics review; PGT-SR for a known translocation follows the same case-by-case path; elective aneuploidy screening on younger patients without a covered indication is usually patient-pay. This page walks through the code set by phase, the diagnosis sequences payers actually accept, how each coverage track handles authorization, and the workflow EasyRCM uses to keep the clinic and lab claims coordinated end-to-end.
PGT Billing by Phase
Representative code examples only. Correct code selection depends on clinical documentation and payer contract terms.
Embryo Biopsy
89290 covers biopsy of 1–5 embryos. 89291 covers biopsy of 6 or more. These codes reflect the embryology labor component only — genetic analysis is billed separately, often directly by the reference lab.
PGT-A (Chromosomal Screening)
81228 is for comparative genomic hybridization (CGH) microarray; 81229 for whole-genome SNP microarray. Payer coverage varies significantly — most commercial plans cover PGT-A for recurrent miscarriage or advanced maternal age only.
PGT-M (Monogenic/Single-Gene)
PGT-M for known single-gene disorders uses 81479 (unlisted molecular pathology procedure) with supporting documentation. Prior auth is almost always required. Lab billing is typically direct-to-lab.
PGT-SR (Structural Rearrangements)
PGT-SR for balanced translocations or chromosomal inversions also uses 81479. Documentation must include the specific structural rearrangement and clinical indication.
Frozen Embryo Transfer (Post-PGT)
After PGT results, the FET cycle is billed with 58976 (frozen embryo transfer). S4017 is used for mandate payers tracking FET cycle utilization. Confirm authorization validity dates — PGT delays sometimes push the FET outside the auth window.
Diagnosis Code Scenarios
ICD-10 codes are illustrative. Final code selection requires clinical documentation review.
PGT-A — advanced maternal age (AMA)
PGT-A — recurrent pregnancy loss
PGT-M — known single-gene disorder
PGT-SR — balanced translocation
How payers cover PGT
Short answer: commercial plans cover PGT case-by-case, keyed to the indication and to whether the analysis is billed globally (through the clinic) or client-billed (directly by the reference lab). Coverage almost never extends to elective aneuploidy screening in patients without a medical indication. The four coverage tracks below have different authorization rules and different diagnosis sequences — and confusing them is the largest single cause of PGT denials.
Medical-indication PGT-A. Advanced maternal age (typically ≥35 or ≥38 depending on payer), recurrent pregnancy loss (two or more losses documented per ASRM's recurrent-loss criteria), or a prior aneuploid pregnancy are the indications most commonly approved. Prior authorization must name the analysis code and the indication together; a request that lists PGT-A without the covered ICD-10 (N96 for recurrent loss, N97.x with the age modifier, or Q95.x for known parental rearrangement) is the standard reason for pre-service denial. Approvals frequently limit the number of embryos analyzed per cycle.
PGT-M and PGT-SR. Case-by-case medical review with genetics documentation. Coverage typically requires a confirmed pathogenic variant in one or both partners (PGT-M) or a documented karyotype showing a balanced translocation or inversion (PGT-SR), plus a genetics counselor's letter of medical necessity. Because these use 81479 (unlisted molecular pathology) rather than a specific PLA code, the pre-auth packet must include a probe design summary and a fee estimate; payers otherwise deny 81479 for lack of code specificity. See the PGT-M and PGT-SR billing walkthrough for the exact documentation set most payers accept.
Fertility benefit managers. Progyny, Carrot, Kindbody, and Maven route PGT through per-cycle allowables. Some FBM contracts fold PGT-A into the base cycle rate as a bundled add-on; others carve it out and reimburse the lab directly under a separate rate schedule. The FBM's authorization letter is the authoritative source for whether the biopsy is billed by the clinic, the analysis is billed by the lab, or both — assume nothing without the letter in the chart. Cycles that unbundle biopsy lines outside the FBM's cycle template draw take-backs even when each individual line is accurate.
Self-pay and elective PGT-A. When no covered indication applies — typically younger patients seeking elective aneuploidy screening — PGT-A defaults to patient-pay. Quote the analysis as a lab-direct charge separate from the clinic biopsy fee so the patient sees the two entities they will owe. Filing an elective PGT-A cycle to major medical without a covered indication draws pre-service denials and, in some contracts, provider-education audits. For a deeper walk-through of the lab-vs-clinic split, see the PGT lab claim conflicts brief.
How EasyRCM bills a PGT cycle
EasyRCM runs PGT through a four-stage workflow — Split → Authorize → Biopsy-bill → Reconcile-and-transfer — that treats the clinic biopsy and the lab analysis as two coordinated claims from the start, and keeps the downstream frozen embryo transfer authorization live through the analysis turnaround.
- Split — establish who bills what at intake. Every PGT case is tagged with the biopsy billing entity (clinic global bill vs. clinic + reference-lab dual bill vs. reference-lab client bill) before the retrieval date. The tag drives the estimate template, the consent packet, and the pre-auth destination — clinic pre-auth for the biopsy line, lab-specific pre-auth for the analysis line, or both.
- Authorize — submit the analysis and biopsy pre-auths as a matched pair. The clinic biopsy request lists 89290 or 89291 with the covered indication ICD-10; the lab analysis request lists the analysis code (PLA or 81479) with the same indication, the number of embryos, and the genetics counselor's letter for PGT-M/SR. Both requests reference the same case ID so the payer's utilization-management team can see them as one clinical episode.
- Biopsy-bill — file the clinic claim on the day of the retrieval-and-biopsy episode. Embryology labor (89290 or 89291) is billed with the IVF retrieval (58970) and cryopreservation lines on a single claim. The analysis is not billed by the clinic under this model — the reference lab bills it separately, with the biopsy specimen accession number cross-referenced on the lab's claim so the payer can pair the two.
- Reconcile-and-transfer — keep the FET authorization inside the analysis window. PGT analysis turnaround typically runs one to three weeks. During that window we confirm the analysis claim adjudicated cleanly, verify the FET authorization has not expired, and — if the analysis pushed the FET past the auth end date — file an authorization extension before the transfer is scheduled. FETs performed on a lapsed auth are the second-largest source of post-PGT denials after mismatched biopsy/analysis indication coding.
Because PGT spans two billing entities and two authorization events, practices that only track the clinic claim almost always miss the second-order failure modes — a paid biopsy line with a denied analysis line, or a cleanly analyzed cohort with an expired FET authorization. EasyRCM reconciles the biopsy claim, the lab's remit, and the FET authorization every week so no case sits with one leg of the episode unfinished.
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