Associations between microsatellite and candidate gene polymorphic markers and the presence of melanoma were analyzed in Old Kladruber greying horses.Fifty microsatellite markers located on 29 out of 31 pairs of horse chromosomes (ECA) and 36 polymorphic markers located in 26 expressed candidate genes (CD14, CTNNAL1, ELA-Eqca-DRA, ELA-Eqca-DQA, FcER1A, GBP1, HRH4, IGHE, IFNG, IL1B, IL1RN, IL4, IL4R, IL10, IL13, IL12A, IL12B, IL12RB2, IL23A, MMP16, TGFB1, TGFB3, TLR4, MC1R, AS1P and STX17) were genotyped.Anal. of genotypes composed of multiple markers not only confirmed single gene associations, but also suggested effects of other immunity-related genes in the presence of melanoma, IL12A, coding for the interleukin-12 p35 subunit and specific major histocompatibility complex Eqca haplotypes.Although some risks of false pos. associations were reduced by corrections for age and multiple comparisons with high P values, the results obtained provide only preliminary evidence that immunity-related genes might be involved in mechanisms of the horse melanoma.The markers identified can be investigated as tools for designing a conservation program aiming to reduce incidence of melanoma without reducing population diversity and specificity.