Detection of susceptibility genes in indirect association studies depends not only on the degree of linkage disequilibrium between the disease variant and the SNP marker but also on the difference in their allele frequencies. Little is known about how variations in these parameters may affect the power of indirect association studies among related populations. Toward this goal, we genotyped 40 SNPs at four loci in samples from three European populations, Galician, Greek, and Norwegian. We compared the relative efficiency of all pairs of SNPs in detecting each other in each one of the populations. Our results show that a low percentage of marker SNPs may detect association in some populations but be totally ineffective in others. Therefore, these differences have to be an additional factor to consider when a replication study fails to confirm initial associations, especially if the replication is focused on very few markers.