The XMR (Xlr-related, meiosis-regulated) protein is an M(r) 30,000 nuclear protein closely associated with the XY body in mouse primary spermatocytes. It shows sequence similarity with several other meiosis-specific proteins. In the present study, we investigated the fine immunolocalization of XMR in the XY body by laser confocal and electron microscopy. It was found that XMR was associated with the asynapsed segments of sex chromosomes, including their axes and the surrounding chromatin loops. In contrast, the pseudoautosomal region and the opposite free end of the X were unlabeled for XMR. In mice with the reciprocal T(X;16)16H translocation, XMR was also associated with the heterochromatic translocation product that emerges from the XY body. These findings at the subchromosomal level point to a role for XMR in chromatin condensation and transcriptional inactivation. XMR is unique among proteins in being capable of association with the XY body. It could play a specific role in a mechanism of male X-chromosome inactivation in mammals.