The superoxide generating NADPH oxidase was studied in an SDS-activated cell-free system. This system requires the participation of both membranal and cytosolic components. Cytosol derived from elicited peritoneal guinea pig macrophages was fractionated by several nucleotide affinity chromatography procedures. Various such fractionations led to the separation of two distinct factors, both of which are necessary for the activation and/or activity of the superoxide-forming NADPH oxidase. One factor (sigma 2), bound to octyl, 2',5'-ADP-, 5'-ATP-, 5'-GTP-agarose and carboxymethyl-Sepharose but did not bind to hexyl, 5'-AMP-, 5'-ADP- and 5'-GDP-agarose. The other factor (sigma 1) did not bind to any of the above matrices. Subsequent elution of sigma 2 from 2',5'-ADP-agarose was effected by ATP, GTP and NADPH but not by NADH. Elution from GTP-agarose was by ATP and GTP but not by NADPH. Elution from ATP-agarose was by ATP, GTP and also, albeit weakly, by NADPH. The above results suggest that sigma 2 contains a site which recognizes the phosphate group at the ribose 2' position in adenosine, and a site that recognizes purine nucleotide triphosphates.