In this study we present a newly detected QTL associated with osteochondrosis in Hanoverian warmblood horses on equine chromosome 18 (ECA18). We developed a highly polymorphic and evenly distributed marker set on ECA18 employing the horse genome assembly EquCab2. The marker set included 11 newly developed microsatellites. Average polymorphism information content was 62.1% at an average spacing of 3 Mb. For genotyping of this marker set comprising a total of 27 highly polymorphic microsatellites, we used the same 14 paternal half-sib families as in the previous whole genome scan. The chromosome-wide linkage analysis revealed a QTL for osteochondrosis in fetlock, hock, or both joints, as well as for osteochondrosis dissecans in hock joints between 74.94 and 82.25 Mb. Within this QTL for equine osteochondrosis, the parathyroid hormone 2 receptor gene could be identified as a positional candidate gene. This report is a further step toward the identification of genes responsible for osteochondrosis in horses.