The HLA gene complex is well known for several reasons, for example, for immunologic studies of peptide presentation, the remarkable polymorphism and the ensuing problems in transplantation, and the association of particular alleles and haplotypes with susceptibility to autoimmune and inflammatory diseases. But for nearly 20 years, there have also been sporadic reports of HLA associations with neural tube defects, spontaneous abortion and infertility, and observations of transmission distortion and deficits of homozygotes. Part of the interest in these reports is because of the identification of developmental genes in or near the murine MHC that affect embryonic and germ cell differentiation. The first part of this review discusses current gene mapping of murine chromosome 17 and human chromosome 6, in light of the spectrum of new genes that have been identified and the colinearity of genes in the two MHCs. The second part scrutinizes published data on HLA associations.