We have examined 23 fibroblast lines from patients with neonatal and late onset glutaric acidemia type II and fibroblasts from four parents of these patients. Fifteen of these patients are previously unreported. Results of these investigations show deficiency of electron transfer flavoprotein or electron transfer flavoprotein-ubiquinone oxidoreductase activity in all of the patients' fibroblasts. Immunoblots indicate that the steady state levels of the antigens is very low or undetectable in most of the neonatal onset patients; however, cross-reacting antigen without electron transfer activity is observed in several glutaric acidemia type II fibroblast lines. Assay of parental lines confirm the autosomal transmission of deficiencies of proteins. Of particular interest is the clinical heterogeneity among these patients. Patients may present with an extrapyramidal movement disorder as observed in glutaric aciduria type I, without the typical organic aciduria typical of glutaric acidemia type II even in the presence of severe enzyme deficiency, or with renal cystic dysplasia accompanying electron transfer flavoprotein deficiency. Renal cystic dysplasia had previously been reported only in patients with electron transfer flavoprotein-ubiquinone oxidoreductase deficiency.