In the present study, we studied the genetic polymorphism in drug transporters, using organic cation/carnitine transporter OCTN2 as a model transporter. Since OCTN2 plays a role in carnitine transport by mediating especially a renal reabsorption of carnitine from urine, free carnitine concentrations in blood and urine were used for phenotyping of the genetic mutation of OCTN2. From general population (n=973), the phenotyping resulted in 46 people with significantly low blood free carnitine concentration. Among them 36 people and 69 normal people were further examined for their free carnitine concentration and OCTN2 genes. Only from the group that showed low carnitine blood concentration, three kinds of heterozygous mutations of OCTN2 gene that show functional loss were found. Furthermore, based on the phenotype observed by systemic carnitine deficiency, many type of mutations in OCTN2 were found with functional loss. Accordingly, organic cations that are transported by OCTN2 are suggested to exhibit altered pharmacokinetic behavior in the people who have the heterozygousity. This is the first demonstration of genetic polymorphism in organic cation transporters found in normal population.