Fully coupled nitric oxide synthase (NOS) catalyzes formation of nitric oxide (NO), L-citrulline, NADP(+), and water from L-arginine, NADPH, and oxygen. Uncoupled or partially coupled NOS catalyzes the synthesis of reactive oxygen species such as superoxide, hydrogen peroxide, and peroxynitrite, depending on the availability of cofactor tetrahydrobiopterin (BH4) and L-arginine during catalysis. We identified three distinct oxygen-induced radical intermediates in the ferrous endothelial NOS oxygenase domain (eNOS(ox)) with or without BH4 and/or L-arginine [Berka, V., Wu, G., Yeh, H. C., Palmer, G., and Tsai, A.-L. (2004) J. Biol. Chem. 279, 32243-32251]. The effects of BH4 and L-arginine on the oxygen-induced radical intermediates in the isolated neuronal NOS oxygenase domain (nNOS(ox)) have been similarly investigated by single-turnover stopped-flow and rapid-freeze quench EPR kinetic measurements in the presence or absence of dithiothreitol (DTT). Like for eNOS(ox), we found different radical intermediates in the reaction of ferrous nNOS(ox) with oxygen. (1) nNOS(Ox) (without BH4 or L-Arg) produces superoxide in the presence or absence of DTT. (2) nNOS(ox) (with BH4 and L-Arg) yields a typical BH4 radical in a manner independent of DTT. (3) nNOS(ox) (with BH4 and without L-Arg) yields a new radical. Without DTT, EPR showed a mixture of superoxide and biopterin radicals. With DTT, a new similar to 75 G wide radical EPR was observed, different from the radical formed by eNOS(ox), (4) The presence of only L-arginine in nNOS(ox) (without BH4 but with L-Arg) caused conversion of similar to 70% of superoxide radical to a novel radical, explaining how L-arginine decreases the level of superoxide production in nNOS(ox) (without BH4 but with L-Arg). The regulatory role of L-arginine in nNOS is thus very different from that in eNOS where substrate was only to decrease the rate of formation of superoxide but not the total amount of radical. The role of DTT is also different. DTT prevents oxidation of BH4 in both isoforms, but in nNOS, DTT also inhibits oxidation of two key cysteines in nNOS(ox) to prevent the loss of substrate binding. This new role of thiol found only for nNOS may be significant in neurodegenerative diseases.