It is presently accepted that, in mammals, due to the greater number of cell divisions in the male germline than in the female germline, nucleotide substitutions occur more frequently in males. The data on mutation bias in insertions and deletions (indels) are contradictory, with some studies indicating no sex bias and others indicating either female or male bias. The sequenced rat and mouse genomes provide a unique opportunity to investigate a potential sex bias for different types of mutations. Indeed, mutation rates can be accurately estimated from a large number of orthologous loci in organisms similar in generation time and in the number of germline cell divisions. Here we compare the mutation rates between chromosome X and autosomes for likely neutral sites in eutherian ancestral interspersed repetitive elements present at orthologous locations in the rat and mouse genomes. We find that small indels are male biased: The male-to-female mutation rate ratio (α) for indels in rodents is ∼2. Similarly, our whole-genome analysis in rodents indicates an approximately twofold excess of nucleotide substitutions originating in males over that in females. This is the same as the male-to-female ratio of the number of germline cell divisions in rat and mouse. Thus, this is consistent with nucleotide substitutions and small indels occurring primarily during DNA replication.