We describe the frequency of Plasmodium falciparum clones infecting individuals living in a rural area of southern Mozambique and analyse the relationship between multiplicity of infection, age and other malariometric indices, including prospective risk of clinical malaria. The genotyping was based on the use of restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) analysis of P. falciparum merozoite surface protein 2 (msp2). We analysed 826 samples collected during five cross-sectional surveys from residents of Manhiça ranging in age from 4 months to 83 years. We also determined the multiplicity of infection in samples obtained from 6-month-old infants (n = 79) and children <10 years (n = 158) who were then treated and followed prospectively for 1 year or 75 weeks, respectively. Multiplicity of infection did not vary significantly during the first year of life, but increased thereafter, and decreased during adulthood to the levels found in infants. With increasing multiplicity of infection, there was a statistically significant decrease in the risk of submicroscopic infections. There was also a significant correlation between multiplicity of infection and parasite density in infants, children <4 years of age and adults, suggesting that high densities increase the probability of discriminating more clones in complex infections. We found that the relationship between multiple infections and malaria morbidity is age-dependent. In infants, the risk of subsequent episodes of clinical malaria was related to the parasite density but not to baseline multiplicity of infection. In older children, however, the more clones a child carried, the more likely they were to have a clinical malaria episode, and this was true after adjusting for parasite densities. This change in the association between multiplicity and risk of clinical malaria may indicate a shift in the host response to P. falciparum.