Defects in ETFB are a cause of multiple acyl-CoA dehydrogenase deficiency (MADD); also known as glutaricaciduria IIB and glutaric aciduria IIB (GAIIB). Glutaric aciduria II (GAII) is an autosomal recessively inherited disorder of fatty acid, amino acid, and choline metabolism.

GAIIB results in the excretion not only of glutaric acid but also of lactic, ethylmalonic, butyric, isobutyric, 2-methyl-butyric, and isovaleric acids. It is seen in its most severe form in infancy, with polycystic and dysplastic kidneys, hypoketotic acidosis and hypoglycemia that can lead to death. The milder form can be characterized by recurrent episodes of lasting lethargy or slowly progressive myopathy.