Advances in gene mapping and genomics in farm animals have been considerable over the past decade. Medium resolution linkage and physical maps have been reported, and specific chromosomal regions and genes associated with traits of biological and economic interest have been identified. We have reached an exciting stage in gene identification, mapping and quantitative trait locus discovery in pigs, as new molecular information is accumulating rapidly. Significant progress has been made by identifying candidate gene associations and low-resolution regions containing quantitative trail loci (QTL). However, we are still disadvantaged by the lack of tools available to efficiently use much of this new information. For example, current pig maps are neither of high enough resolution nor sufficiently informative at the comparative level for positional candidate gene cloning within QTL regions. As well, studying biological mechanisms underlying economically important traits such as reproduction is limited by the lack of molecular resources. This is especially important, as reproduction is very difficult to genetically improve by classical breeding methods due to the relatively low heritability and high expense in data collection. Thus, an improved understanding of porcine reproductive biology is of crucial economic importance, yet reproductive processes are poorly characterized at the molecular level. Recently, new methodologies have been brought to bear on a better understanding of pig molecular biology for accelerating genetic improvement in pigs. Several groups are developing molecular information in the pig, and the total Genbank sequence entries for porcine expressed genes have recently topped 100,000. Our Midwest EST Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited nearly 15,000 gene sequences into public databases. These sequences represent over 8,900 different genes, based on sequence comparison among these data. Furthermore, we have developed computer software to automatically extract sequence similarity of these pig genes with their human counterparts, as well as the mapping information of these human homologues. Within our data set, we have identified nearly 1,500 pig genes with strong similarity to mapped human genes, and we are in the process of mapping 700 of these genes to improve the human-pig comparative map. This work and the complementary work of others can now be used to more rapidly understand and identify the genes controlling reproduction, so that genetic improvement of reproduction phenotypes can accelerate.