There are many genetic variations in the human genome. The most abundant form of genetic variation is the single nucleotide polymorphism (SNP). SNPs are thought to be responsible for observable differences in biological processes among individuals of a population. Genetic association studies utilizing SNP markers are expected to allow identification of genetic factors responsible for complex phenotypes like chronic diseases and responses to various nutritional elements. Success of such studies relies on detecting genetic markers either directly responsible for the phenotype or the markers with a close relationship with causative markers. There are over 10 million SNPs reported and each SNP contains limited genetic information due to the limited number of alleles. To cover these limitations, researchers have to genotype many SNP markers to find appropriate associations. As a result, the need for efficient high-throughput SNP genotyping technologies is high and many efficient high-throughput SNP genotyping technologies have been developed. Highly efficient systems that can handle as many as 500,000 SNPs at a time have been developed and technological advances have transformed genome-wide association studies into reality.