We established a maternal birth cohort in Ibadan, Nigeria, where malaria is hyperendemic, to assess how intrauterine exposure to malaria affected infant blood pressure (BP) development. In a local maternity hospital, healthy pregnant women had regular blood films for malaria parasites from booking to delivery. Growth and BP were measured on 318 babies, all followed from birth to 3 and 12 months. Main outcomes were standardized measures of anthropometry and change in BP to 1 year. Babies exposed to maternal malaria were globally smaller at birth, and boys remained smaller at 3 months and 1 year. Change in systolic BP (SBP) during the year was greater in boys than in girls (20.9 versus 15.7 mm Hg;P=0.002) but greater in girls exposed to maternal malaria (18.7 versus 12.7 mm Hg; 95% confidence interval, 1–11 mm Hg; P=0.02). Eleven percent of boys (greater than twice than expected) had a SBP ≥95th percentile (hypertensive, US criteria), of whom 68% had maternal malaria exposure. On regression analysis (β coefficients, mm Hg), sex (boys>girls; β=4.4; 95% confidence interval, 1.1–7.7; P=0.01), maternal malaria exposure (3.64; 0.3–6.9; P=0.03), and weight change (2.4; 0.98–3.8/1 standard deviation score; P=0.001) all independently increased SBP change to 1 year, whereas increase in length decreased SBP (−1.98; −3.6 to −0.40). In conclusion, malaria-exposed boys had excess hypertension, whereas malaria-exposed girls a greater increase in SBP. Intrauterine exposure to malaria had sex-dependent effects on BP, independent of infant growth. Because infant–child–adult BP tracking is powerful, a malarial effect may contribute to the African burden of hypertension.