The structure of bovine heart mitochondrial NADH dehydrogenase was investigated by using 2 cleavable cross-linking agents, disuccinimidyl tartrate and (ethyleneglycol)ylbis-(succinimidylsuccinate). Cross-linking was analyzed primarily by immunoblotting to detect products containing subunits of the Fe-protein fraction from chaotropic resolution of the enzyme, namely, those of 75, 49, 30 and 13 kDa [dalton]. By using both the isolated Fe protein fraction and the intact dehydrogenase, cross-links were identified between these 4 subunits, from these subunits to the largest subunit of the flavoprotein fraction, which contains the active site for NADH and from these subunits to polypeptides in the hydrophobic shell, which surrounds the hydrophilic Fe protein and flavoprotein fractions.