The effects of malaria and anaemia during pregnancy on infant survival and morbidity were investigated in an area of low malaria transmission on the western border of Thailand. A cohort of 1,495 mothers and their infants were followed weekly from admission of the mother to ante-natal clinics until one year of life of the infant. 37% (555/1495) of the women developed malaria during pregnancy and 77% (1134/1468) were anaemic (HCT<30%). Malaria during pregnancy was responsible for 23% (95% Confidence Interval: 14-30) of Low Birth Weight (LBW), but did not reduce the duration of gestation. Infectious diseases in the week prior to birth were associated with premature birth (Population Attributable Fraction: 10%; 95%CI: 6-12). Infant mortality rate was 78 (88/1127) per 1,000 live births. Risk factors for neonatal mortality were prematurity (Hazard Ratio: 9.8; 95% Cl: 3.8-25.2), LBW (HR: 2.9; 95%CI: 1.2-7.3), and maternal infection in the week prior to delivery (HR: 4.3; 95%CI: 2.0-9.2). The latter remained associated with deaths occurring between one and three months of age (HR: 4.0; 95%CI: 1.2-13.7), whereas no risk factors could be identified for deaths occurring later in infancy. Malaria during pregnancy affected neonatal mortality solely by lowering birth weight, whereas fever in the week prior to birth had an additional independent effect as well as inducing premature birth. Malaria incidence rate in infancy was low: 121 (148/1228) per 1,000 child-year (95%CI: 103-142). The stage of pregnancy at which malaria occurred influenced malaria in infants. Infants bom to mothers who had falciparum malaria during the first trimester were 2.8 (1.5-5.1) times more likely to develop malaria in infancy, than infants bom to mothers who had malaria later during pregnancy, or no malaria. The long-term impact of malaria during pregnancy on the infant was mediated through LBW that was associated with higher morbidity, anaemia and impaired growth. However, as age increased, socio-economic factors became more important than LBW for the development of infant anaemia and for the risk of being underweight and/or stunted.