A phenotypic female aged 15 4/12 years was referred because of delayed puberty and short stature. Chromosomal analysis of peripheral blood leukocytes revealed two subpopulations of cells. The modal cell line was hypodiploid with a missing X chromosome while the other cell line was diploid with one X chromosome and a G-sized chromosome that resembled a Y chromosome in morphology. Subsequent fluorescent in situ hybridization yielded results consistent with the above conventional cytogenetic studies. To provide unequivocal evidence of the Y-chromosome material, molecular analyses using the polymerase chain reaction and various primers were carried out which identified an intact short arm and centromere of the Y chromosome and structurally altered long arms. A laparoscopic bilateral gonadectomy, performed because of the risk of neoplasia, also yielded cells with both 45,X and 46,XY karyotypes. The present report thus illustrates the usefulness of a combined approach for diagnosing delayed puberty.