Flavin-containing monooxygenases (FMOs) represent the second most important human monooxygenase system, after cytochrome P450s (CYPs) and catalyze the oxygenation of many chemicals containing nitrogen-, sulphur-, phosphorous-, selenium-and other nucleophilic heteroatoms. FMO3 is the prominent FMO form in adult human liver. For FMO3, both interindividual variability within a single ethnic group and variability between ethnic groups have been reported. In our study, three prevalent functional FMO3 variants (E158K, V257M, and E308G) were genotyped in healthy Turkish people by polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) methods. The frequencies of alleles and haplotypes were compared with those obtained from different populations. It was found that FMO3 158K, 257M and 308G alleles, demonstrate impaired metabolism toward many FMO3 substrates, were observed frequently in Turkish population similar to the other populations. Also, the frequencies of haplotypes were determined based on individual allelic frequencies and it was observed that the most common haplotypes were haplotip EVE and KVE (E158K/V257M/E308G), which together accounted for 80% of all haplotypes. The obtained data from the present study could be useful for further studies assessing sensitivity to therapeutic drugs, environmental toxicants and common disease.