The mouse Y Chromosome (Y Chr) map has developed considerably since the last report. The generally accepted size of 60 Mb for the Y Chr has been called into question, as the C57BL/6J Y Chr has been measured to contain 94.7 Mb of DNA (46799). Fifteen new anonymous Y-specific markers have been derived but have not been sublocalised on the chromosome (46799). Three new genes have also been placed on the map. The genetic map of the Y Chr suggests that all its critical functions are involved in spermatogenesis. These are further divided into spermiogenesis functions (Smy) on the long arm and pericentric region, and mitotic germ cell proliferation functions (Spy) located on the minute short arm. A rich transcription map has been developed in the Sxrb deletion interval which is known to contain Spy. The position and relative order of genes, anonymous markers and chromosomal breakpoints are presented on the Chromosome Committee map. As the Y Chr does not recombine along most of its length, the cM values were applied arbitrarily to reproduce the order derived by physical mapping.