Hybridization of Y chromosome-specific probes to Southern blots of genomic deoxyribonucleic acid from patients with chromosomal variants permits direct and rapid characterization of the chromosomal content. We have used two single-copy Y chromosomal sequences specific for the short arm (47z and DP34) and one repeated sequence specific to the long arm (Y3.4) to study several patients with different types of sex chromosomal abnormalities, including three patients with gonadal dysgenesis and the karyotype 45,X/46,X + fragment, two females with Y autosomal translocations involving similar regions of the Y chromosome (46,XX,t(Y;14)(q11,p11) and 46,XY,t(Y;15)(q11,p11), two males with very small Y chromosomes (del(Y)(q12) and i(Yp], and a 45,X male with a small Y autosomal translocation. These techniques are more sensitive than chromosome banding and thus are an important adjunct to karyotyping for analysis of chromosomal content. For patients with gonadal dysgenesis and uncharacterized fragments, demonstration of Y chromosomal sequences identifies an important risk factor for the development of gonadoblastoma. For other patients, accurate identification of Y chromosomal content may facilitate prediction of the patient's phenotype.