The presence of Y-chromosomal sequences in the cells of patients with Turner-Syndrome (TS) is a risk factor for the development of gonadal tumors. Therefore and since demonstration of Y-material usually results in prophylactic gonadectomy optimal sensitivity and specificity of the diagnosis have to be attempted. We wanted to evaluate the diagnostic potential of cytogenetic investigations as routinely employed in TS. In the most comprehensive study published so far we screened 208 TS patients for the presence of Y-chromosomal sequences by polymerase chain reaction (PCR) specific for eight different loci along the Y-chromosome. Six patients (3%) without cytogenetic evidence of Y-chromosome were found to be Y-positive. Among 12 cases with marker chromosomes two more Y-chromosomal fragments were identified. Thus, PCR-screening for Y-specific sequences was shown to be a valuable tool in the clinical management of Turner patients.