Osteochondrosis dissecans is a particularly common developmental orthopaedic disorder in equines. Among its causes, the hereditary component is no longer a matter of debate, and, for several decades, the various studbooks for sport horses have been selecting stallions in order to limit the prevalence of this condition in the population. However, to our knowledge, no study has evaluated changes in the prevalence of osteochondrosis dissecans over time through longitudinal monitoring of a population of sport horses. The study presented here is part of a large screening programme for developmental orthopaedic pathologies in Wallonia (Belgium) and assessed the presence of these lesions over a period of 19 years in the Walloon sport horse population according to constant and standardised sampling and diagnostic criteria. The effects of breeding conditions and infection in foals were also assessed by means of questionnaires. The results showed no significant change in the prevalence of osteochondrosis dissecans in a population of 1099 individuals born between 2004 and 2022. Furthermore, individuals who had suffered from sepsis during their growing period were very significantly predisposed (p < 0.001) to the development of osteochondrosis dissecans compared to a control group, with respectively 14/21 (67%) and 103/364 (28%) of individuals affected. This study suggests that the selection programmes applied to the population studied are not sufficiently strong or adapted to reduce the prevalence of osteochondrosis dissecans in the population over a period of 19 years. Moreover, this study confirms that foals with sepsis and concurrent osteochondrosis dissecans lesions should not necessarily be excluded from breeding programmes on this basis.