The identification of different morphometric patterns of spermatozoa serves as a basis for improving our understanding of the diversity in an ejaculate and to relate them to the potential fertility of males. In this study, we aimed to examine the semen subpopulation structure, following dilution in semen of extenders, using a mathematical approach a possible application to fertility analyses. Ten sexually mature Bos taurus bulls were randomly allotted to one of three groups: (1) Tris-citric acid-egg yolk extender (Tris-EY); (2) commercial egg yolk extender OptiXcell® and (3) commercial egg yolk extender Triladyl®. The results showed significant differences (p < .05) between extenders in terms of values for head size and head shape variables of individual sperm, indicating an influence of extender composition. Sperm head width was found to significantly differ (p < .05) according to the extender, decreasing in the following order: OptiXcell® (4.836 ± 0.017 μm), Triladyl® (4.695 ± 0.012 μm) and Tris-EY (4.638 ± 0.010 μm). Principal component analysis allowed us to identify two subpopulations in OptiXcell®, and three subpopulations were each found in Triladyl® and Tris-EY. Overall, we observed significant differences between sperm subpopulations within each extender (p < .05), with differences in sperm head size and shape between bovine species that can be related to functionality and fertility capabilities.