We report here that mouse embryos can exhibit a significant incidence of blastomere fragmentation at the two-cell stage. The incidence of this is influenced by both the maternal and paternal genotype. Embryos from C57BL/6 mothers exhibit a very low incidence of fragmentation at the two-cell stage in crosses involving males of C57BL/6, DBA/2, AKR/J, or SJL strains but exhibit a significantly increased incidence of fragmentation in crosses involving C3H/HeJ males. Increased fragmentation is seen in embryos from C3H/HeJ females crossed with C57BL/6 males but not with C3H/HeJ males. Embryos obtained from reciprocal (C57BL/6 x C3H/HeJ) F1 hybrid females also exhibit an increased incidence of fragmentation at the two-cell stage when the hybrid females are mated to either C57BL/6 or C3H/HeJ males. Interestingly, the results differ significantly between reciprocal F1 hybrid females, indicating a parental origin effect, possibly a result of either genomic imprinting or differences in mitochondrial origin. We conclude that the incidence of blastomere fragmentation at the two-cell stage in the mouse is under the control of more than one genetic locus. We also conclude that blastomere fragmentation is affected by both parental genotypes. These results are relevant to understanding the genetic control blastomere fragmentation, which may contribute to evolutionary processes, affect the success of procedures such as cloning, and affect the outcome of assisted reproduction techniques.