Osteochondrosis (OC) is common in large-breed dogs. According to the breeding guidelines of the Swiss kennel clubs, the shoulder joints are included in the radiographic screening for joint diseases in the Greater Swiss Mountain dog (GSMD) and the Border Collie (BC) since 1993 and 2003, respectively. The aim of this study was to estimate the overall prevalence of humeral head OC in these 2 breeds in Switzerland based on the data of the Swiss National Dysplasia Committees. All radiographs were re-evaluated to assess single radiographic changes. From 1993 and 2003, accordingly, until 2013, the overall prevalence was 14% for the GSMD and 8% for the BC, respectively. Affected joints showed a focally reduced opacity or a flattened/indented contour of the caudal section of the humeral head. Articular flaps were only seen occasionally. Degenerative joint disease was significantly more common in OC affected joints (GSMD: 32%; BC: 20%) than in joints without OC. The present study is the first report on the prevalence of humeral head OC in a large cohort of GSMD and the BC over a long study period. In comparison to other breeds, the herein reported prevalences are in the mid to upper range. Results of the present study should alert veterinarians to the disease in these breeds and may serve as a starting point for further epidemiological and genetic studies.