A polymerase chain reaction (PCR) assay which detects a sex-based polymorphism in the bovine amelogenin locus was modified and compared to conventional cytogenetic analysis for diagnosis of freemartinism (XX/XY chimerism) in cattle. The PCR assay is more sensitive than cytogenetic analysis for detection of XY cells, with the limit of detection of the assay falling between 0.2% and 1% XY cells. Seventy-three heifer blood samples submitted for evaluation of freemartinism to the University of Minnesota Diagnostic Laboratory were tested using both cytogenetic and PCR techniques. Poor-quality samples precluded successful lymphocyte culture and recovery of mitotic nuclei for cytogenetic evaluation in 17 cases (23%). Two of these samples (2.7%) also failed to amplify with PCR. There was 100% agreement in the results from the 56 samples that were suitable for testing using both techniques. This PCR-based assay provides an alternative to the more laborious cytogenetic evaluation for diagnosis of freemartinism.