bComplex I (NADH ubiquinone oxidoreductase) is a large multisubunit enzyme that catalyzes the first step in oxidative phosphorylation (OXPHOS). In mammals, complex I biogenesis occurs in a stepwise manner, a process that requires the participation of several nucleus-encoded accessory proteins. The FAD-dependent oxidoreductase-containing domain 1 (FOXRED1) protein is a complex I assembly factor; however, its specific role in the assembly pathway remains poorly understood. We identified a homozygous missense mutation, c.1308 G¡A (p.V421M) in FOXRED1 in a patient who presented with epilepsy and severe psychomotor retardation. A patient myoblast line showed a severe reduction in complex I, associated with the accumulation of subassemblies centered around ϳ340 kDa, and a milder decrease in complex II, all of which were rescued by retroviral expression of wild-type FOXRED1. Two additional assembly factors, AIFM1 and ACAD9, coimmunoprecipitated with FOXRED1, and all were associated with a 370-kDa complex I subassembly that, together with a 315-kDa subassembly, forms the 550-kDa subcomplex. Loss of FOXRED1 function prevents efficient formation of this midassembly subcomplex. Although we could not identify subassemblies of complex II, our results establish that FOXRED1 function is both broader than expected, involving the assembly of two flavoprotein-containing OXPHOS complexes, and cell type specific.T he oxidative phosphorylation (OXPHOS) system is responsible for the generation of the majority of cellular ATP. NADH ubiquinone oxidoreductase (complex I), the first enzyme in the pathway, is responsible for the oxidation of NADH. This is coupled with the pumping of protons across the inner mitochondrial membrane, contributing to the formation of the electrochemical gradient that is ultimately used by ATP synthase (complex V) to generate ATP.Complex I is embedded in the inner mitochondrial membrane, forming an L-shaped structure with a membrane domain and a peripheral domain that protrudes into the mitochondrial matrix. It is composed of 44 structural subunits, 7 of which are encoded by the mitochondrial genome (mitochondrial DNA [mtDNA]). In mammals, complex I biogenesis occurs in a stepwise fashion by sequential addition of assembly intermediates (1). Assembly of the holoenzyme requires the import of the 37 nucleus-encoded subunits, followed by sorting, folding, and assembly into the appropriate structural domain of the complex. Seven iron-sulfur clusters are incorporated into five of the core subunits of the peripheral arm (NDUFS1, NDUFS7, NDUFS8, NDUFV1, and NDUFV2), and a flavin mononucleotide (FMN) molecule is inserted noncovalently into NDUFV1.Deficiencies in the activity of complex I, among the most common causes of OXPHOS disorders, are associated with a wide variety of clinical phenotypes that can range from lethal infantile diseases to isolated myopathy or adult-onset neurodegenerative disorders (2). Mutational analyses have identified defects in all 14 core subunits and several of the so-called supernumerary s...