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Abstract We established a set of 30 microsatellites of Bovidae origin for use in a biodiversity study in Swiss and Creole goats. Additional microsatellites located within or next to "candidate" genes of interest, such as cytokine genes (IL4, INF-gamma) and MHC class II genes (DRB, DYA) were tested in the caprine species in order to detect possible associations with two infectious caprine diseases. Microsatellite analysis was undertaken using automated sequencers (ABI373 & 3100). In the first study, a total of 82 unrelated Creole goats, 37 resistant and 45 susceptible to Heartwater disease (Cowdriosis) were analysed. In this study, the two microsatellite loci DRBP1 (MHCII) and BOBT24 (IL4) were positively associated with disease susceptibility, demonstrating a corrected P-value of 0.002 and 0.005, respectively. In a second investigation, we tested 36 goats, naturally infected with the nematode parasite Trichostrongylus colubriformis. These animals were divided into a "low" and "high" excreting group on the basis of two independently recorded fecal egg counts. For this nematode resistance study, we detected a significant association of one of the alleles of the microsatellite locus SPS113 with "low" excretion (resistance). The MHC class II locus DYA (P19), was weakly associated with susceptibility in both diseases (Pc = 0.05). In future experiments, we will extend the sample size in order to verify the described associations.