The mechanism of NADH oxidation varies between living organisms, and is by far the most complex oxidizing system found in mitochondria. In human mitochondria, a unique, but huge structure, with more than 45 subunits, known as complex I, copes with NADH oxidation. This review compiles our present knowledge on the organization of this complex and the putative role of a small subset of its subunits. This review also describes the major progress that has been made in understanding the molecular bases of respiratory chain complex I deficiency in humans, with mutations identified in both the mitochondrial and the nuclear genes encoding complex I subunits. Finally, the puzzling questions raised by the varying clinical presentations of patients with complex I deficiency are discussed in light of our limited knowledge on complex I function in mammalian cells.