Association between malaria and pregnancy complications, such as prematurity, intrauterine growth restriction, low birthweight and infant mortality has been reported. These effects have been studied widely in areas hyperendemic for malaria, but studies in low-endemic areas are scarce. The study investigated the relation between gestational malaria and low birthweight and intrauterine growth retardation in neonates of a malarial endemic region in Colombia, between 1993 and 2007.The pattern of development in 1,716 neonates of women with and without malaria infection during pregnancy was evaluated in a cohort study. A total of 394 infected (27% by P. falciparum and 73% by P. vivax) and 1,322 noninfected pregnant women were followed.Exposure to gestational malaria was associated with increased risk of low birth weight (RR = 1.37; 1.03-1.83), short height (RR = 1.52; 1.25-1.85), intrauterine growth retardation (RR = 1.29; 1.0-1.66) and prematurity (RR = 1.68; 1.3-2.17). Prematurity was 77% higher in infants of mothers with malaria by P. falciparum than infants of mothers with malaria by P. vivax (RR = 1.77; 1.2-2.6).Low birth weight and intrauterine growth retardation were associated with malaria during pregnancy. Infection with P. vivax was related with adverse effects on the newborn, similar to that reported for P. falciparum.