The aim of the study was to evaluate the influence of the chromosome Y structure and Trp53 genotype on semen quality parameters. Mice with partial deletion of the Y chromosome (B10.BR-Y-del) have severely altered sperm head morphology when compared with males that possess the complete Y chromosome (B10.BR). Control males from B10.BR and B10.BR-Y-del mice, and mutant males from B10.BR-p53(-/-) and B10.BR-Y-del-p53(-/-) experimental groups were used. We assessed testis weight, sperm head abnormalities, viability of spermatozoa (eosin test), percentage of motile and immature sperm, and performed a hypo-osmotic test to detect abnormal tail membrane integrity. Sperm morphology and maturation were controlled by the genes within the deleted region of the Y chromosome. Testis weight was higher in the mutants than in the control males, possibly due to cell accumulation in Trp53-deficient males as the concentration of sperm was significantly increased in the mutants. An elevated percentage of abnormal sperm was noted in B10.BR-p53(-/-) and B10.BR-Y-del-p53(-/-) male mice. We suggest that, in Trp53-deficient mice, the sperm cells that escape apoptosis are the ones that have abnormal morphology. The only sperm quality parameter affected by the interplay between Trp53 and chromosome Y genes was sperm motility, which was elevated in B10.BR-p53(-/-) males, but remained unchanged in B10.BR-Y-del-p53(-/-) males.