Computed tomography (CT) is commonly used for imaging the equine head, particularly when diseases of temporomandibular joint (TMJ), including osteoarthritis (OA), are suspected. However, certain CT findings have been proposed as 'anatomical variations', and their clinical significance remains unknown. The objectives of this prospective descriptive cross-sectional study were to describe the CT and histopathological findings of TMJ OA in relation to horse age, evaluate the accuracy of TMJ OA diagnosis with regard to 'CT anatomical variations', and explore the correlations between specific CT and histopathological findings. CT images and tissue samples from 41 heads (82 TMJs) were independently and simultaneously reviewed by two observers. Descriptive statistics on both findings, their age-related frequency, and accuracy of TMJ OA diagnosis were calculated. Based on histopathological assessment, TMJ OA was confirmed in 18% of joints in horses aged 1-4 years, 63% of joints in horses aged 5-15 years, and 83% of joints in horses over 15 years. Considering entire CT findings, TMJ OA was radiologically recognized in 76% of joints, with a sensitivity of 0.95 and a specificity of 0.37. When 'CT anatomical variations' were excluded, TMJ OA was recognized in 30% of joints, with a sensitivity of 0.51 and a specificity of 0.88. Findings suggest that the equine TMJ may undergo both age-related and disease-related remodeling, detectable through CT and histopathology, and that the inclusion or exclusion of certain 'CT anatomical variations' in the diagnostic protocol affects the sensitivity and specificity of CT-based TMJ OA recognition.