Over the past decade the tools of modern molecular biology have provided unique insights into our fundamental understanding of developmental systems. These insights have been gleaned from the study of a wide variety of model organisms including yeast (Saccharomyces cerevisiae), fly (Drosophila), worm (Caenorhabditis elegans), and mouse. In man, the first analysis of developmental systems started with sexual differentiation and focused on the role of Y-linked genes. The presence of living developmental mutants in man affecting sexual development and the early technology of deletion mapping facilitated the isolation and identification of small segments of putative DNA suspected to contain sex-determining genes. The isolation of genes such as SRY (Sex Related gene on Y) has provided the first insights into the molecular biology of human sexual differentiation. The focus on the Y chromosome has brought further insights into chromosomal pairing, statural determinants in man, oncogenesis, spermatogenesis, haploid genomes, and the lineage of man himself. This paper provides the circumstantial and direct evidence to illustrate the importance of the Y chromosome in reproductive disorders, and in the analysis of haploid genomes.