We describe the initial characterisation of a Drosophila melanogaster locus, Mst40 (Male-specific transcript), that was cloned on the basis of its male-specific transcription during the third larval instar. Corresponding low molecular weight poly(A)+ mRNAs are abundant in primary spermatocytes, but in no other larval or adult tissue. During early embryogenesis Mst40 expression is complex; initially transcription is detected during early cleavage stages. This early expression appears as two discrete dots of hybridisation associated with each nucleus. Subsequently, the transcripts are abundant in the cytoplasm of the newly formed pole cells. In the genome Mst40 sequences are located in region 40, at the base of chromosome 2L, close to, or within, the beta-heterochromatin. The Mst40 sequences are organised as a tandemly arrayed 1.4 kb repeat unit. The repeat is conserved in all D. melanogaster strains examined but absent from other Drosophila species studied. The locus does not correspond to any known complementation groups in the region and has yet to be assigned a function.