The XY body is a structure formed by the partially synapsed chromosomes X and Y that is located at the nuclear periphery of mammalian pachytene spermatocytes. In contrast to the autosomal bivalents of the same nucleus, the XY body is characterized by its differential chromatin condensation and transcriptional inactivity. In order to shed some light on the biological significance of these differences we have been characterizing XY body-associated proteins. We present here the cDNA sequence and expression pattern of XY40, a protein that is associated with the axial elements of the XY body. RNA blot analysis revealed that during spermatogenesis the transcript that encodes protein XY40 was highly enriched in pachytene spermatocytes. This transcript was also detectable in brain and, to a lesser extent, in liver and kidney. Although the signal in brain was as strong as in spermatocytes, protein XY40 could be detected only in the latter. The nucleic acid sequence reveals that XY40 is a novel protein with a few similarities to already known nucleotide sequences. Among these similarities the most interesting is a box that is shared by the 3' untranslated region of XY40 and the 5' untranslated region of Munc-18c, a member of a protein family involved in synaptic vesicle exocytosis. Since the transcripts of both XY40 and Munc18-c show a similar expression pattern, it is tempting to speculate that this common sequence is involved in translation regulation.