Sperm morphology reflects a long process of adaptation to external conditions and the barriers encountered before ova fertilization can take place; however, not all morphological variation found in gametes can be explained by the effects of these selective forces, as the genetic component may also contribute to the establishment of different gametic features. In north-eastern Spain, there is a wide Robertsonian system of Mus musculus domesticus, where individuals with 2n ranging from 27 to 40 chromosomes have been described. To elucidate the effect of the karyotype on sperm head form, a comparative analysis between different chromosomal groups of mice from this zone was carried out. Sperm heads from eight St (2n = 40) and 24 Rb (2n = 30–39) males were processed for scanning electron microscopy and analysed using geometric morphometric techniques. Canonical variate analyses showed substantial shape differences between St and Rb mice in the ventral spur region and between Rb groups in the post-acrosomal region. Significant differences in sperm head size were also detected between chromosomal groups. Structural disorders related to spermatogenesis, genetic alterations, and epistatic interactions among loci are probably involved in the relationship between the phenotypic variation of the sperm head and Rb translocations. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110, 878–889.