Computed tomography (CT) is an established technique for detecting shoulder lesions in dogs, however the clinical significance of shoulder CT lesions often remains uncertain. The purposes of this retrospective study were to describe the prevalence of CT lesions in both shoulder joints for 89 dogs presenting with thoracic limb lameness and to compare CT lesions with clinical characteristics. For all included dogs, results of a full orthopedic examination, other diagnostic tests, and signalment data were available in medical records. Multilevel, multivariable logistic regression was used to test clinical significance of the most prevalent CT lesions and determine factors associated with their presence. Computed tomographic lesions were detected in one or both shoulder joints for 51/89 dogs (57.3%). Mineralization of one or more surrounding peri-articular soft-tissue structures was identified in 31.5% of dogs, with supraspinatus muscle/tendon mineralization being the most frequently identified (24.7%). The prevalence of humeral head osteochondrosis was 9 and 21.3% of dogs had shoulder osteoarthritis. Border collies (odds ratio [OR] 9.3; 95% CI 1.39–62.1, P = 0.02) and dogs with shoulder pain (OR 4.3; 95% CI 1.08–17.1, P = 0.04) had increased risk of osteochondrosis lesions. Border collies (OR 8.4; 95% CI 1.27–55.6; P = 0.03) and older animals (OR 1.04; 95% CI 1.02–1.1, P < 0.001) had increased risk of osteoarthritis lesions. Female entire dogs had an increased risk of supraspinatus mineralization lesions (OR 6.8; 95% CI 1.55–29.5, P = 0.01). Findings indicated that shoulder CT lesions are common in dogs with thoracic limb lameness, and that some CT lesions are not associated with shoulder pain.