X/Y male mice carrying the sex reversal factor, Sxr, on their Y chromosomes typically produce 4 classes of progeny (recombinant X/X Sxr ♂♂ and X/Y non-Sxr ♂♂, and non-recombinant X/X ♀♀ and X/Y Sxr ♂♂) in equal frequencies, these deriving from obligatory crossing over between the chromatids of the X and Y during meiosis. Here we show that X/Y males that, exceptionally, carry Sxr on their X chromosome, rather than their Y, produce fewer recombinants than expected. Cytological studies confirmed that X-Y univalence is frequent (58%) at diakinesis as in X/Y Sxr males, but among those cells with X-Y bivalents only 38% showed normal X-Y pseudo-autosomal pairing. The majority of such cells (62%) instead showed an illegitimate pairing between the short arms of the Y and the Sxr region located at the distal end of the X, and this can be understood in terms of the known homology between the testis-determining region of the Y short arm and that of the Sxr region. This pairing was sufficiently tenacious to suggest that crossing over took place between the 2 regions, and misalignment and unequal exchange were suggested by indications of bivalent asymmetry. Metaphase II cells deriving from meiosis I divisions in which the normal X-Y exchange had not occurred were also found. The cytological data are therefore consistent with the breeding results and suggest that normal pseudo-autosomal pairing and crossing over is not a prerequisite for functional germ cell formation. The data support the concept that Y short arm-Sxr pairing and crossing over may be the mechanism responsible for the occurrence of the Sxr variants reported in the literature.