The simultaneous production of superoxide and nitric oxide by stimulated human neutrophils leads to the formation of peroxynitrite, a physiologically important bactericidal agent. We have investigated two possible pathways for the inactivation of inducible nitric oxide synthase (NOS-II) by peroxynitrite:  inactivation of NOS-II through oxidation of the tightly bound cofactor calmodulin (CaM) and direct interaction of ONOO^-/ONOOH with the NOS-II protein. Studies of two model peptides indicated that the Ca²⁺-dependent binding to CaM of a typical high-affinity sequence, melittin, significantly prevented Met oxidation in CaM by ONOO^-/ONOOH. In contrast, binding of the putative CaM-binding domain of human hepatocyte NOS-II (NOS-II_509-534) to CaM only marginally prevented the oxidation of Met residues in CaM. When the native NOS-II/CaM complex was exposed to peroxynitrite, CaM was inert toward oxidation. Nevertheless, even small amounts of peroxynitrite abolished the activity of NOS-II through direct interaction with the heme. The loss of activity was paralleled by a decrease in heme absorbance and a shift of the absorbance maximum from 419 to 409 nm. The presence of the cofactor tetrahydrobiopterin during peroxynitrite exposure did not prevent inactivation of the enzyme but altered the change of the heme spectrum, i.e., a shift of λ_max from 419 to 420 nm rather than to 409 nm. In conclusion, peroxynitrite inactivates NOS-II through changes in the heme or its environment in NOS-II rather than via oxidation of the cofactor CaM.