Developmental Orthopaedic Disease (DOD) in limb joints of horses is frequent and is a common cause of pain and lameness. DOD is a multifactorial disease involving genetics, growth, feeding practices and exercise conditions leading to joint injuries. However, there is no clear understanding of the contribution of each factor. The aim of this cohort study was to assess the adjusted effects of breed and gender, growth, feeding practices and exercise conditions on the prevalence of DOD in the limbs of foals at weaning and on the prevalence restricted to osteochondrosis (OC). Twenty-one farms in Normandy, France, were convenience sampled and enrolled in a cohort study. The study sample consisted of 401 foals from 3 breeds, followed from the 8th month of pregnancy of the mares until weaning period at approximately 6 months of age of the foals. Stud farms were regularly visited to collect growth, feeding practices and exercise conditions data. The carpus, the front and hind digits, the hock and the stifle of the foals were X-rayed at the end of follow-up. Foals were categorised as affected or unaffected by DOD or by OC. Two mixed-effects logistic regression models were used to determine risk factors for DOD or OC, adjusting for clustering by farm. Of the 378 foals with complete data, 47% (95% CI: 42–52) were affected by DOD and 36% (95% CI: 31–41) by OC. Risk was significantly increased for DOD and for OC in Warmblood foals compared to Thoroughbreds (OR 2.8; 95% CI: 1.2–6.5 for DOD, OR 2.9; 95% CI: 1.1–7.5 for OC), in foals with a high wither height at 30 days of age, and in foals with a rapid increase of wither height (for DOD only). Exercise conditions such as large area of pasture, some irregular exercise, or some batch changes were also significant risk factors for DOD or OC. No association was found with quantitative feeding practices; it was likely due to the limited variability of horse regimens and to the partial inclusion of nutritional effects in other factors such as breed and growth. In order to reduce the prevalence of DOD or OC in foals, following the growth and reducing nutritional supply in subjects growing fast, limiting the pasture areas offered and providing a regular exercise to foals seems appropriate. To our knowledge, to date the assessment of adjusted effects of potential risk factors for DOD has never been proposed.