The thermodynamic and EPR characteristics of the iron-sulfur clusters of NADH-ubiquinone oxidoreductase have been examined in various subfractions and subunits of the enzyme. These were obtained by fragmentation of the enzyme with chaotropic agents and detergent and salt fractionation. We provide evidence for the presence of three tetranuclear clusters and five or six binuclear clusters, accounting well for the chemically determined iron content of this enzyme (22-24 atoms/molecule of FMN). Some of the clusters can be identified with EPR-detectable species in intact NADH-ubiquinone oxidoreductase and, by combining information on subunit topography and spin-spin interactions between redox centers in the native enzyme, we propose a tentative scheme for the spatial organization of these iron-sulfur clusters in the enzyme and in the membrane.