ABSTRACT In order to learn more about the role of sex chromosome-dependent gene products in gonadogenesis, changes in protein patterns were studied during gonadal development. Two-dimensional gel electrophoresis analysis revealed specific proteins in both sexes at all developmental stages. Evidently the gonads are not indifferent by biochemical criteria at any developmental stage and express several specific genes from the onset of differentiation. To correlate these polypeptides with the sex chromosomes, proteins were investigated in human-rodent somatic cell hybrids and in genetically identical cell clones differing in one sex chromosome only. On two-dimensional gels one Y-dependent polypeptide was found with similar characteristics (relative molecular mass and isoelectric point) as an early testicular polypeptide. Its identity, however, remains to be proven.