Nicotine metabolism rates differ widely, even after controlling for genetic variation in the major nicotine metabolizing enzyme, CYP2A6. Genetic variants in an additional nicotine metabolizing enzyme, flavin containing monooxygenase (FMO)-3, and an obligate microsomal CYP-supportive enzyme, cytochrome P450 oxidoreductase (POR), were investigated. We examined the impact of FMO3 E158K and POR A503V, before and after stratifying by CYP2A6 metabolism group. In 130 non-smokers of African descent who received 4 mg oral nicotine, FMO3 158K trended towards slower nicotine metabolism in reduced CYP2A6 metabolizers (P=0.07) only, whereas POR 503V was associated with faster CYP2A6 activity (nicotine metabolite ratio) in normal (P=0.03), but not reduced, CYP2A6 metabolizers. Neither FMO3 158K nor POR 503V significantly altered the nicotine metabolic ratio (N=659), cigarette consumption (N=667), or urine total nicotine equivalents (N=418) in smokers of African descent. Thus, FMO3 E158K and POR A503V are minor sources of nicotine metabolism variation, insufficient to appreciably alter smoking.