There is evidence from Y Chromosome (Chr) deletion mapping that there is a gene on the long arm of the mouse Y Chr that is needed for the normal development of the sperm head. Since mice with partial Y long arm deletions show incomplete penetrance of the sperm head defect, whereas mice with no Y long arm show complete penetrance, it has been suggested that the 'spermiogenesis' gene may be present in multiple copies. A Y-specific genomic DNA sequence (Y353/B) has previously been described that is present in multiple copies on the long arm of the mouse Y and identifies testis-specific transcripts. We have suggested that Y353/B could be the proposed multiple copy 'spermiogenesis' gene. In support of this suggestion, we show here that mice with a partial Y long arm deletion associated with a 3.5-fold increase in the frequency of abnormal sperm heads have a marked reduction in genomic Y353/B copies and a corresponding reduction in Y353/B-related transcripts. Thus, the incompletely penetrant phenotype correlates with a reduction in Y353/B-related transcription. Furthermore, by in situ hybridization with a Y353/B riboprobe to testis sections, we show that the Y353/B-related transcripts are confined to the round spermatid stage of spermiogenesis, just prior to the shaping of the sperm head. The transcripts sediment with the fraction of cytoplasmic RNA in adult testis that is loaded on polysomes, suggesting that the transcripts are actively translated.