The first part of this review (Lancet 2000; 355: 299) covered primary disorders of mitochondrial DNA (mtDNA). This section will cover nuclear-encoded defects of the oxidative phosphorylation (OXPHOS) system, including mtDNA mutations that are secondary to nuclear gene mutations and nuclear gene defects responsible for secondary OXPHOS deficiency (panel). The latter group of diseases are predominantly neurodegenerative. The mitochondrion's role in apoptosis and its contribution to the pathogenesis of neurodegenerative diseases are also covered.