BCS1L is a chaperone necessary for the incorporation of Rieske FeS and Qcr10p into complex III (CIII) of the respiratory chain. Mutations in the BCS1L gene cause early fetal growth restriction and a lethal neonatal disease in humans, however, the pathogenesis remains unclear. Here, we analysed the expression of BCS1L during mouse embryonic development and compared its expression with that of the mitochondrial markers Porin, GRIM19, Core I, and Rieske FeS. BCS1L was strongly expressed in embryonic tissues already at embryonic days 7 (E7) and 9 whereas the expression of Porin and Rieske FeS was not as evident at this time point. At E11, BCS1L, Porin, and Rieske FeS had overlapping expression patterns in organs known to contain high numbers of mitochondria such as heart, liver and somites. In contrast, BCS1L was differently distributed compared to the mitochondrial proteins Porin, Rieske FeS, Core I and Grim 19 in the floor plate of the E11, E12 and E13 neural tube. These results show that the expression pattern of BCS1L only partially overlaps with the expression of Porin and Rieske FeS. Thus, BCS1L alone or in cooperation with Rieske FES may during development have previously unknown functions beside its role in assembly of complex III. The floor plate of the neural tube is essential for dorsal ventral patterning and the guidance of the developing neurons to their targets. The predominant expression of BCS1L in this region, together with its presence in peripheral ganglia from E13 onwards, indicates a role for BCS1L in the development of neural structures.