The purpose of this study was to examine the presence of linkage disequilibrium between nine microsatellite loci in and out of Major Histocompatibility Complex (MHC) as a description of population structure in White Karaman, Awassi and Merinolandschaf sheep populations. Of the 108 pairwise comparisons a significant linkage disequilibrium was observed between six and seven loci pair after exact test and pooling, respectively. Only two and three of the significant deviations were present between MHC-linked loci. The results indicated that the populations analyzed in this study were mostly in equilibrium and that selection did not play a major role to maintain the linkage disequilibrium between MHC-linked loci in the populations studied.