Fibroblast extracts and fetal liver homogenates from patients with propionic acidemia due to inherited deficiency of propionyl CoA carboxylase (PCC) were analyzed for the presence of immunologically cross-reactive PCC protein. Using several rabbit antisera raised against homogeneous human liver PCC, homogeneous pig heart PCC, or the individual non-identical subunits of the human liver enzyme, we found no detectable cross-reacting material by direct or competitive immunotitration in several cell lines from patients in either major complementation group (pcc A; pcc C) with isolated PCC deficiency. In contrast, cells of a patient from the bio complementation group contained normal amounts of immunoreactive PCC. Further analysis of the pcc A and pcc C mutants revealed that their residual propionyl CoA carboxylating activity varied greatly depending on the concentration of extract or homogenate protein used in the PCC assay. When propionyl CoA carboxylation was assayed at high protein concentration in a fetal liver homogenate from a pcc C patient, the apparent PCC activity was comparable to that found in normal human fetal liver. Significantly, the specific activity in the mutant, but not in the control, extract declined steeply as protein concentration was lowered, and this loss could not be prevented by adding PCC substrates, bovine serum albumin, glycerol, or 2-mercaptoethanol. Moreover, detailed analyses of immunotitration curves of control fibroblasts extracts showed that fresh extracts contained an amount of nonimmunotitratable carboxylating activity corresponding to the residual activity present in fresh extracts of mutant cell lines. We conclude that the residual propionyl CoA carboxylating activity found in isolated PCC deficiency represents another carboxylase that can utilize propionyl CoA as a substrate rather than a mutant form of PCC with markedly different immunochemical and physicochemical properties.