The skull is a vitally important complex structure formed by the combination of many bones. Craniometric studies are performed with various imaging methods to determine morphometric characteristics in animals. One of these methods is radiography. In our study, skulls of 14 Hamdani sheep, 20 Siirt‐coloured mohair goats and 20 Romanov sheep breeds were used. Skull sections were taken with a computed tomography device and saved in DICOM format. Nine separate measurements and six index calculations were made from the images. In the study, firstly, the gender difference was ignored and the similarities and differences between the species were recorded. In addition, gender differences were determined statistically, without making any distinction between species. Correlation analysis was performed to compare measurement parameters between animal species. As a result of the study, the highest skull length (SL) and cranial length (CL) values were determined in the Siirt‐coloured mohair goat. It was determined that the difference between Romanov sheep and Siirt‐coloured mohair goat in CL parameter was not statistically significant (p > 0.05). In addition, a statistically significant difference was observed between the Romanov sheep breed and the Hamdani sheep breed (p < 0.01). The external length of the cranium (ELC) measurement parameter was found to have a statistically significant difference in three animals (p < 0.01). According to the results of the correlation analysis, the highest correlation value was determined between cranial width (CW) and CL parameters (r = 0.920). When the species difference was ignored, and the statistical difference of the internal height of the cranium (IHC) parameter was found to be significant between female and male animals (p < 0.05). In addition, it was determined that SL, CW and internal cranium index (ICI) parameters had a significant difference depending on sex (p < 0.01). It is foreseen that the obtained data can be used in sciences such as zoo archaeology, anatomy, surgery and forensic medicine.