Patients with clinical features of Turner's syndrome may have a 45,X/46,X + mar or 46,X + mar karyotype. It is estimated that phenotypic females or intersexuals with a Y chromosome and gonadal dysgenesis have a 20% risk of developing gonadoblastoma, so it is crucial to know whether Turner's syndrome patients have a Y chromosome. We studied the chromosomal make-up of four patients with Turner's syndrome using the polymerase chain reaction (PCR). Nine Y-chromosomal loci including four loci (PABY, SRY, ZFY, DYS14) on the short arm, one loci (DYZ3) on the centromere, and four loci (DYS132, DYS1, DYZ1, DYZ2) on the long arm were amplified to determine the origin of marker chromosomes. Three patients were identified as having Y chromosome DNA. Patient 1 contained the presumed gonadoblastoma locus (DYS132) and a prophylactic gonadectomy was carried out. DNA extracted from dysgenetic gonads did not show Y chromosome DNA. A rapid, highly sensitive and isotope-free method for detection of abnormal Y chromosomes in Turner's syndrome patients has been developed. Chromosome in situ hybridization analysis is required to confirm the PCR results, to provide further evidence for molecular organization of these marker chromosomes.