Pharmaco-genomics determines the individual genetic mechanism for drug response and has the ability to transform tailored medication into clinical practice. A huge number of individuals die every year from adverse drug response since each person reacts differently to similar drug. The science of pharmaco-genomics has emerged as a potential discipline in the development of drugs and clinical medicine during the last several decades. It has offered a hope of protection for the patients against lethal health complications that arise from the adverse drug responses. The new medication approaches utilizing the science of pharmaco-genomics reduce the patient exposure to less or non-effective drugs or drugs with adverse effects. Same drugs have been reported to induce specific reactions in each individual owing to different nucleotide sequences in genes that encode the essential biological molecules such as drug-metabolizing enzymes, drug transporters, and drug targets. Single nucleotide polymorphisms (SNPs) are very helpful in determining the susceptibility of individuals to different diseases and drug reaction. These polymorphisms are the most prevalent in the genome of humans and account for 90% of genetic variance amongst individuals. Pharmaco-genomics may help in understanding the strong effects of inherited single gene variations on drug mobilization and action. The detection and characterization of SNPs related with disease risk and adverse drug response (ADR) is essential before using them as genetic tools. The credibility of SNP application in the diagnosis of diseases and possible ADR has been increased by the completion of HapMap project but still there are some challenges associated with it. The present chapter attempted to present the general role and effect of SNPs on pharmaco-genomics as well as their utility in clinical practice.