Protamines are small, very basic, sperm-specific proteins condensing sperm chromatin during spermiogenesis. Sexual selection acts on protamines in a complex manner, with a balance between maintenance of protein function and directed positive selection. This seems to relate to the potential effects of protamine changes on sperm head morphology and sperm swimming performance. In species with low levels of sperm competition, chromatin condensation and protection of DNA from damage appear to be the basic role of protamines. On the other hand, in species with high sperm competition levels, shaping of the sperm head may represent an additional, major role, which may affect hydrodynamic efficiency. Our previous studies provided initial evidence for the hypothesized effect of protamines on sperm head size and shape in rodents. We have now examined protamine 1 gene sequences throughout mammals and identified sexual selection acting on gene sequence, and a relation with sperm head size. However, this effect seems to be complex and highly variable within mammalian orders and families. Considering the differential selection acting on protamine gene sequence across mammals we assessed possible differences in the relation between protamine expression, regulatory sequences and head shape among rodent families and whether they are underlied by differential selection. We found that sexual selection seems to favour a higher protamine ratio in mice (Muridae) and a lower protamine ratio in voles (Cricetidae). This is reflected in the lineages head shapes and dimensions. These results underscore the difficulty to identify roles of sexual selection on protamines or other proteins influencing sperm competitive traits. In order to understand how certain head shapes are favoured in mice while other shapes are favoured in cricetids, studies on the interplay of nucleus shape, hook morphology, sperm metabolism, and patterns of flagellar beating will be required.