The molecular pathways leading from indifferent mammalian gonad to either testis or ovary are not well understood. A number of genes, including the Y-linked sex determining gene SRY, have been shown to play roles in sex determination or differentiation, but there are clearly many missing elements to be found. We used suppression-subtractive hybridization to construct normalized cDNA libraries enriched for male-specific or female-specific transcripts in mouse fetal gonads. We describe the strategy used to efficiently screen these libraries for candidate sex-determination and gonadogenesis genes. One gene arising from these screens is vanin-1, which encodes a protein implicated in the induction of cell migration into the thymus. We find that vanin-1 is expressed male-specifically in Sertoli cells of the developing testis and may be involved in inducing cell migration from the adjacent mesonephros, a process known to be critical for testis development. This screening approach is likely to be applicable to the isolation and study of genes involved in a variety of developmental systems.