The charge heterogeneity of the mitochondrial acetyl-CoA acetyltransferase (EC 2.3.1.9), referred to transferases A and B, seems to be preformed in vivo and can be demonstrated it7 vitro by a spontaneous transformation of transferase A into transferase B. These two enzymes, although remarkably similar in amino acid composition, show structural dissimilarities. This becomes evident from their tryptic maps, which are substantially different.Isoelectric focusing in the presence of urea confirms the charge heterogeneity of the mitochondrial acetyl-CoA acetyltransferase by indicating different patterns of protein bands for transferases A and B. Transferase B lacks the protein band with an isoelectric point of 7.2 which is normally shown with transferase A. However, this 7.2-pl protein band can be demonstrated after a [3H]CoASH treatment of transferase B in the presence of urea by protein staining and by autoradiography. This change in the isoelectric focusing band pattern after interaction of the subunits with CoASH is interpreted as being the result of an apparently covalent secondary modification of the protein side chains.The CoASH-modification may be the only molecular basis of the acetyl-CoA acetyltransferase charge heterogeneity, a view, which is further substantiated by the CoASH-mediated transformation of transferase B into transferase A. An additional heterogeneity of the enzyme as caused by a limited proteolysis seems unlikely but cannot be definitely excluded.The liver mitochondrial acetyl-CoA acetyltransferase which catalyzes the first step in the biosynthebis of ketone bodies has been shown to exist in at least three distinct forms [ I -71. Transferases A and B, the two main forms from rat liver, revealed immunochemical cross-reactivity but both proved to be immunologically unrelated to the cytosolic acetyl-CoA acetyltransferase and the mitochondrial acetylCoA acyltransferase. Transferases A and B represent variously charges stated of the mitochondrial acetyl-CoA acetyltransferase protein. This has been shown by the isoelectric points of 8.5 and 9