Abstract Background Pathological fractures have been reported in equids with pituitary pars intermedia dysfunction (PPID) but their prevalence and pathogenesis is unknown. Objectives To compare: (1) bone mineral density (BMD) in weight bearing and nonweight bearing bones in PPID + equids and aged and young PPID − controls; and (2) biomechanical properties of the fourth lumbar vertebral body in PPID + equids and aged PPID − equids. Study design Case–control study: five PPID + equids and six aged and four young PPID − control horses. Methods PPID status was based on clinical signs and necropsy examination of the pituitary gland (PG). The lumbar vertebral column, right front third metacarpus (MC3), left hind third metatarsus (MT3), and PG were removed after euthanasia. BMD was determined by quantitative computed tomography of regions of interest (ROI) in each bone and biomechanical testing was performed on the fourth lumbar vertebral body. Serum concentrations of parathormone (PTH), ionised Ca ++ , 25‐hydroxyvitamin D, and osteocalcin (OC) were also measured. Data were analysed using one‐way ANOVA and correlation analyses. Results BMD of trabecular and cortical regions of interest (ROI) of the third, fourth (L4), and fifth lumbar vertebrae were significantly lower in PPID + equids as compared with aged ( p < 0. 001) and young ( p < 0.01) PPID − controls. In contrast, no differences were found in BMD of trabecular or cortical ROIs of MC3 and MT3 between groups. No differences were detected in force at fracture, displacement at fracture, Young's modulus or strain of L4 between PPID + and aged PPID − horses. No differences were found in serum PTH, ionised Ca ++ , 25‐hydroxyvitamin D, or OC concentrations between groups. Main limitations Limited number of equids studied and variation in test results. Conclusions BMD of nonweight bearing bones can be decreased with PPID and could increase risk of developing pathological fractures.