Here we review the rationale for considering the pyruvate dehydrogenase multienzyme complex (PDC) as a target for gene therapy for defects in mitochondrial energetics. PDC is entirely nuclear encoded and is situated in the mitochondrial inner membrane. The complex catalyzes the rate-determining step in aerobic carbohydrate metabolism and plays a critical role in the efficient conversion of substrate fuel into energy by cells. PDC activity is regulated in large part by reversible phosphorylation (inactivation) of its E1α subunit. Congenital defects in PDC are usually due to mutations in E1α and are typified by lactic acidosis, neurodegeneration and early death. Acquired deficiency in PDC has been implicated in the etiopathology of several other metabolic or neurodegenerative disorders. Recently, a vector using recombinant adeno-associated virus (rAAV) that contained a fusion protein of full-length E1α and the reporter gene green fluorescent protein was used to deliver wild type E1α into mitochondria after injection of the construct in vivo into the central nervous system of rats and in vitro into human cells. Transduction of cultured fibroblasts from a male patient with E1α deficiency led to partial restoration of PDC activity, as determined by decarboxylation of 14C-pyruvate. These data indicate that at least partial correction of PDC defects may be feasible by gene transfer. Furthermore, the combination of AAV-mediated delivery of E1α with pharmacologic activation (dephosphorylation) of the wild type enzyme subunit may provide an optimal therapeutic strategy for patients with acquired or congenital deficiencies in mitochondrial energy metabolism.