This study aims to investigate morphological differences in the skulls of cattle breeds with different functional roles and geographical origins and to examine skull shape variations among breeds using geometric morphometrics methods. To this end, 95 skulls from Native (Eastern Anatolian Red and Southern Anatolian Red) and Non-native (Holstein and Simmental) breeds raised in Türkiye were analyzed. The results show a significant size difference between Native Breeds and Non-native Breeds, with the Non-native Breeds having larger skulls. The results also indicate considerable shape differences between Native and Non-native Breeds. No significant shape differences were observed between the two Native Breeds, which have shared the same geography for many years. Although no statistically substantial size difference was found between Simmental and Holstein, the nuchal region showed distinct shape differences. The nuchal part of the Simmental skull was more pronounced than other specimens. In native breeds, there was a more balanced proportion between the facial and neurocranial regions compared to the other two breeds. In Holstein skulls, the facial region was more pronounced in comparison to the neurocranial region, while in Simmental skulls, the neurocranial region was more prominent. This study provides valuable insights into the morphological characteristics of different cattle breeds, contributing to veterinary anatomy, biology, and paleontology.