The bovine Y chromosome (BTAY) map has been developed considerably in recent years. There are approximately 260 DNA markers, including ~50 MS, 10 genes/ESTs, and ~200 BES, on BTAY. These markers together with their associated RH map and BAC fingerprinted contigs provide the basic materials for the future sequencing of BTAY. Several bovine homologs of human Y chromosome genes have been isolated. These genes are found to be expressed mainly or only in the testis, which opened the door for molecular approaches to the study of spermatogenesis and subfertility/infertility in bulls. The outcomes of such studies will probably lead to the design of new marker-assistant selection (MAS) strategies for male fertility to select sires at an early age in breeding programs.