A 15.5-year-old female was referred for primary amenorrhea and slow development of secondary sex characteristics. The karyotype revealed 45,X/46,X,+mar (75%/25%). The small marker chromosome was C-band and Q-band negative. It appeared to be primarily centromeric with some light G-band staining material on either side. Females with Y-chromosomal material are at an increased risk for gonadal neoplasia and this patient was studied further to investigate the possibility that the marker was a deleted Y chromosome. Polymerase chain reaction (PCR) analysis of this patient's DNA revealed the presence of Y-chromosomal material presumably derived from the marker chromosome. These results indicate that the PCR technique, in conjunction with cytogenetic analysis, can identify possible Y-chromosomal material. This testing provides critical information necessary for correct medical followup of Turner syndrome mosaic patients.