Flavin-containing monooxygenases (FMO) represent the second most important human monooxygenase system, after cytochrome P450. However, its importance is underestimated. This review summarized the distinctive characteristics of FMO3, including its function, genetic variation, regulation,application, etc. The population differences of FMO3 were also reviewed. Based on the above progress, the future strategy of FMO study in drug development was suggested.