Navicular disease or podotrochlosis is one of the main causes of progressive forelimb lameness in warmblood horses. The objective of this study was to refine a quantitative trait locus on horse chromosome 2 for radiological alterations in the contour of the navicular bone (RAC) in Hanoverian warmblood horses. Genotyping was performed in 192 Hanoverian warmblood horses from 17 paternal half-sib groups. The marker set was extended to 58 informative microsatellites including nine newly developed microsatellites. QTL for RAC could be delineated at 32.50-43.13 Mb and a further new QTL for RAC could be identified at 59.08-65.14 Mb. The markers ABGe342 and ABGe343 reached the highest multipoint Z(mean) and LOD scores at 34.42 and 35.23 Mb with genome-wide error probabilities of P = 0.013 and P = 0.064. In addition, significant associations of markers and haplotypes within the QTL could be shown. The results support the location of the QTL on ECA2 associated with RAC. This work is a further step towards the development of a marker test for navicular disease in Hanoverian warmblood horses.