Osteochondrosis (OC) is a focal disturbance of endochondral ossification due to a failure of blood supply to the epiphyseal growth cartilage. In dogs, OC most commonly affects the shoulder joint, followed by the elbow, tarsal, and stifle joints. The condition is associated with clinical signs such as lameness and pain and the prognosis varies depending on the affected joint. Most epidemiologic studies of OC in dogs were performed over 20 years ago, and updated estimates of disease incidence are lacking. Therefore, the objectives of this study were to provide population-based estimates of the incidence rate, cause-specific mortality rate, and age at diagnosis of appendicular OC (AOC, including OC of the shoulder, elbow, stifle, and tarsal joints) and stifle and tarsal OC separately, using data from Agria Djurförsäkring in Sweden (2011–2016). Further, the study aimed to evaluate the risk of OC in subgroups divided by breed and sex and describe previous, concurrent, and subsequent diagnoses of the affected joint in dogs with stifle or tarsal joint OC. The study population included just over 600,000 dogs, of which 685 were affected by AOC. Stifle joint OC (n = 113) was more common than tarsal joint OC (n = 80). The incidence rate of AOC was 3.77 (95% confidence interval (CI): 3.49–4.07) cases per 10,000 dog-years at risk, while the incidence rate of stifle and joint tarsal OC was 0.64 (95% CI: 0.53–0.77) and 0.43 (95% CI: 0.34–0.54) cases per 10,000 dog-years at risk, respectively. All breeds at increased risk of AOC were large or giant, and male dogs had an increased risk of AOC compared to female dogs (RR 1.76, 95% CI: 1.50–2.07, p < 0.001). The median age at first diagnosis during the study period was 0.74 (0.32–11.5) years for AOC, 2.62 (0.45–8.82) years for stifle joint OC, and 0.73 (0.35–7.35) years for tarsal joint OC. Of the dogs with stifle or tarsal joint OC, 30.2% and 15.0% had a previous diagnosis of stifle/tarsal joint pain or other unspecific clinical signs, respectively, and 13.8% of the dogs with stifle joint OC suffered subsequent cruciate ligament rupture. Osteochondrosis was the most common reason for euthanasia in the affected dogs. In total, 77 dogs were euthanised due to AOC during the study period.