Several full-length clones encoding the human and guinea pig orthologs of flavin-containing monooxygenase 5 (FMO5) have been isolated from libraries constructed with hepatic mRNA. The clones were detected by hybridization with the cDNA encoding FMO5 expressed in rabbit. The human and guinea pig cDNAs encode for proteins of 533 amino acids that contain putative pyrophosphate binding domains characteristic of mammalian FMOs. The sequences derived for the human and guinea pig FMO5 proteins are 87% identical and are 85 and 82% identical, respectively, to the sequence of rabbit FMO5. As is the case with other FMOs, FMO5 in human and guinea pig is encoded by multiple transcripts. Rabbit FMO5 expressed in Escherichia coli was purified and used to elicit antibodies in goat. These antibodies detected FMO5 in samples from livers of adult humans, rabbits, and guinea pigs and fetal livers of humans. The human and guinea pig forms of FMO5 were expressed in E. coli and characterized. Neither enzyme effectively catalyzed the metabolism of methimazole, a general FMO substrate; however, both were active with n-octylamine. The responses of the human FMO5 and guinea pig FMO5 to detergent, ions and elevated temperature are all similar to the responses described for rabbit FMO5. These results indicate that the unique properties of FMO5 from rabbit are species-independent and that this form of the flavin-containing monooxygenase is not readily classified as a drug-metabolizing enzyme.