The combination of single nucleotide polymorphisms (SNPs) database and high-density SNP array allows the use of SNPs as informative polymorphic markers for Mendelian diseases with complex traits efficiently. With the high-density and high-resolution SNP arrays, we can detect even the smallest structural changes that would have been missed with conventional low-density cytogenetic techniques for prognostic and diagnostic utilities. Accurate mapping may be useful for genotype-phenotype correlation in individual basis and for prenatal investigations. Here, we review some applications of genome-wide SNP genotyping on detecting homozygous candidate region in consanguineous family priors to mutation analysis. In addition to personalized genomic medicine, studying the genetic heterogeneity in diverse ancestral population helps to implementing effective clinical management.