The NAD(+)-dependent isocitrate dehydrogenase of Saccharomyces cerevisiae is an octamer composed of four Idh1p subunits and four Idh2p subunits. Isocitrate dehydrogenase functions in the tricarboxylic acid cycle and has also been reported to bind to the 5' nontranslated region of mitochondrially encoded mRNAs. Mutants defective in either or both of these subunits are unable to grow on the nonfermentable carbon source, acetate, but will utilize glycerol or ethanol. Mutant strains lacking Idh2p maintain normal if not elevated levels of mitochondrial Idh1p. In addition to the mature unassembled Idh1p subunit, a complex of bands in the 85- to 170-kDa range (Idh1p-Cpx) is observed using NAD-IDH antiserum. Both Idh1p and Idh1p-Cpx are insoluble within the mitochondrion and are associated with the mitochondrial inner membrane. A histidine-tagged form of Idh1p was expressed in yeast strains. Chemical amounts of the Idh1p-Cpx could be purified from strains lacking Idh2p but not from strains containing normal levels of Idh2p. The data indicate that Idh1p-Cpx is an aggregated and cross-linked form of Idh1p that may be oxidized within the mitochondrion as a consequence of its aborted assembly.