Longitudinal genetic analysis of the composition of malaria parasites infecting humans has demonstrated that individuals living in endemic areas are chronically infected with multiple genotypes and species of Plasmodium. The accumulation of infections is a consequence of superinfection from the bites of many infected anopheline mosquitoes. The clinical outcome of infection is determined by the host's ability to regulate the density of malaria parasites in the blood. Interestingly, most infections do not cause symptoms of malarial disease after a degree of immunity is acquired. Here, we review data from the first genetic study of the longitudinal dynamics of multiple Plasmodium species and genotypes in humans. The data show that the total parasite density of Plasmodium species oscillates around a threshold and that peaks of infection with each species do not coincide. We propose that malaria parasitaemia is controlled in a density-dependent manner in these semi-immune children. This implies that a cross-species mechanism of parasite regulation exists. A model of how multiple immune responses could act in concert to explain these within host dynamics is discussed in relation to known regulatory mechanisms.