Genetic polymorphisms in superoxide-producing NAD(P)H oxidase have been linked to cardiovascular diseases including anthracycline-induced cardiotoxicity. We quantified NAD(P)H oxidase activity in granulocytes of 81 healthy Caucasian volunteers (in addition, 51 in an independent confirmatory study) by chemiluminescence using the luminol analogue L-012. Expression of CYBA, NCF4 and RAC2 coding for NAD(P)H oxidase subunits was measured in whole blood cells in 59 study participants by realtime PCR. Of the five variants investigated (À930A4G, 242C4T, 640A4G in CYBA and the recently reported À368G4A in NCF4 and 7508T4A in RAC2), only CYBA 640A4G was consistently associated with superoxide production (640GG carriers 28% less than AA individuals, P ¼ 0.05 in each cohort, P ¼ 0.005 in combined analysis). RAC2 7508T4A was related to higher expression of RAC2 (P ¼ 0.02) and NCF4 (P ¼ 0.04). In summary, CYBA 640A4G rather than 242C4T was associated with reduced activity. The quantitatively moderate effect and the high intra-individual variability should be considered for further study design.