The pathogenesis of severe, Plasmodium falciparum malaria in African children is considered in the context of its two major clinical syndromes: malaria with respiratory distress; and malaria with neurological disturbance. Respiratory distress is an important prognostic marker in children with P. falciparum infections. In the majority of cases it reflects an underlying metabolic acidosis, usually associated with lactic acidaemia. Hypovolaemia and anaemia are important underlying factors. The syndrome of malaria with neurological impairment is not a homogenous condition. Four distinct groups of children fulfilling the WHO definition of cerebral malaria may be distinguished: (1) prolonged post-ictal state; (2) covert status epilepticus; (3) severe metabolic derangement (particularly hypoglycaemia and metabolic acidosis); and (4) children with a primary neurological syndrome. These distinctions are important from a therapeutic point of view, as well as for their implications for studies on underlying pathogenic factors. A simple framework is presented to summarize how three major processes, anaemia, the acute phase response and sequestration of infected cells, may interact to lead to reduced tissue oxygenation as a unifying process in the pathogenesis of both major clinical syndromes of severe malaria.