Septic arthritis is common in newborn calves due to poor birth and housing hygiene. This study investigated the pathological deformities caused by arthritis in the carpal bones of calves using geometric morphometry. The changes in the carpal joint bones of newborn calves with septic arthritis were examined through shape analysis. The study included 20 healthy Simmental calves and 30 Simmental calves with septic arthritis. Dorso‐palmar x‐ray images of the carpal joint were taken, and geometric morphometry was performed on these images using 25 landmarks. The first principal components (PC1) represented 26.92% of the total variation, while PC2 represented 13.84%. One of the most significant shape changes with increasing PC1 occurred in the os carpi intermedium. The study found that it was statistically possible to discriminate between radiometric carpal joint images of Simmental calves in the control and arthritis groups using geometric morphometry. In newborn calves with septic arthritis, the trochlea radi was located more proximally. There was an enlargement of the os carpi intermedium and a tendency towards the os carpi ulnare in female calves with septic arthritis. These results indicate significant bone deformation due to septic arthritis. Geometric morphometric methods can be clinically useful, as demonstrated in this study. Researchers can statistically explore these shape analyses, opening new avenues for research in this field. This method not only enhances our understanding of morphological changes but also provides a framework for clinical investigations and discoveries in related areas.