We estimated the incidence of clinical malaria episodes by weekly home-based active case detection between December 1996 and July 1999 in 2 groups of children in Manhiça district in southern Mozambique. Cohort 1 comprised a random sample of children aged <10 years at recruitment and cohort 2 comprised newborns. A blood slide was taken if the axillary temperature was 7.5 degrees C or if the child was reported to have been febrile over the previous 24 h. A total of 1966 children were followed-up. Malaria occurred all year round. The number of clinical malaria episodes ranged from 0 to 6 per child. No clinical malaria episodes were detected in 71% of children or in children aged <2 months. Those aged 6 months to <4 years showed the highest incidence ranging from 0.65 to 0.74 episodes per 100 person-weeks at risk, indicating that infants and young children were at highest risk. Malaria transmission is perennial in this district of Mozambique with some seasonality. Significant differences were observed in the spatial incidence of malaria episodes in regions just a few miles apart with a higher incidence in children living near the river or in swampy areas. These findings strengthen the need for improved control measures targeted at infancy and early childhood.