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Abstract Background Perineal hernia (PH) is a relatively common condition in intact male dogs, but the etiology remains unclear. The objective of this study was to assess the contribution of gastrointestinal (GI), neurological, and orthopedic conditions to the development of PH in male dogs. Patient history with a focus on chronic GI disease was assessed using an owner questionnaire. Neurological conditions were explored, applying neurological, electromyographic (EMG), and motor nerve conduction velocity (MNCV) examinations and combining these with computed tomography (CT) imaging. To exclude possible orthopedic diseases, an orthopedic examination was conducted together with CT analysis. The chi-squared test was used to assess the associations between categorical variables. Results Altogether, 66 male dogs with diagnosed PH were recruited for this study. The frequency of neurological, orthopedic, and GI diseases was low in dogs with PH. No signs of generalized neuro- or myopathies were detected. Still, perineal and bulbourethral reflexes were decreased or missing in 44.6% (29/65) and 40.0% (26/65) of dogs, respectively. Mild or moderate occlusion of the intervertebral foramen at the lumbosacral (LS) junction occurred in 18.5% (12/65) of dogs and was caused by spondylosis deformans in 83.3% (10/12). Moderate disc protrusion was evident in 9.2% (6/65) of dogs. Conclusion No evidence was found that PH is caused by gastrointestinal, orthopedic, or neurological conditions. Abnormalities in perineal and bulbourethral reflexes are most likely secondary to PH.