Electron transfer flavoprotein (ETF) is a heterodimeric enzyme composed of an alpha-subunit and a beta-subunit and contains a single equivalent of FAD per dimer. ETF deficiency can be demonstrated in individuals affected by a severe metabolic disorder, glutaric acidemia type II (GAII). In this study, we have investigated for the first time the molecular basis of beta-ETF deficiency in three GAII patients: two Japanese brothers, P411 and P412, and a third unrelated patient, P485. Molecular analysis of the beta-ETF gene in P411 and P412 demonstrated that both these patients are compound heterozygotes. One allele is carrying a G to A transition at nucleotide 518, causing a missense mutation at codon 164. This point mutation is maternally derived and is not detected in 42 unrelated controls. The other allele carries a G to C transversion at the first nucleotide of the intron donor site, downstream of an exon that is skipped during the splicing event. The sequence analysis of the beta-ETF coding sequence in P485 showed only a C to T transition at nucleotide 488 that causes a Thr154 to Met substitution and the elimination of a HgaI restriction site. HgaI restriction analysis on 63 unrelated controls' genomic DNA demonstrated that the C488T transition identifies a polymorphic site. Finally, transfection of wild-type beta-ETF cDNA into P411 fibroblasts suggests that wild-type beta-ETF cDNA complements the genetic defect and restores the beta-oxidation flux to normal levels.