In the last 30 years the amount of white markings in the population of Franches-Montagnes horses (FM) has more than doubled which has led to some controversy, particularly in respect to the health of the horses. The objective of this study was to investigate if the coat colour and white markings have an impact on selected skin diseases and hoof horn abnormalities. To this purpose 974 three-year-old FM were subjected to a clinical examination during the field and station tests organized by the FM breeding association. In 16.9% of the horses, one or several equine sarcoids were detected, 15.2% of the horses showed clinical signs of pastern dermatitis, 1.1% of insect bite hypersensitivity and 18.0% of dermatitis of other aetiology. Abnormalities of the hoof horn were found in 20.1% of the horses. The prevalence of pastern dermatitis was 2.6 times higher in legs with white markings than in legs with pigmented skin (p <0.0001). The probability ofsuffering from sunburn and hoof horn of lesser quality was increased in animals with an elevated white marking index (WAI; p = 0.022 and p = 0.038), on the other hand, horses with sarcoids had a significantly lower WAI than sound horses (p = 0.038). Our study shows that FM horses with more pronounced white markings have an increased risk to suffer from pastern dermatitis, sunburns and hoof horn abnormalities. The coat colour was not associated with skin diseases.