Background . In areas where malaria is endemic, infants aged <3 months appear to be relatively protected from symptomatic and severe Plasmodium falciparum malaria, but less is known about the effect of Plasmodium vivax infection in this age group.

Methods . To define malaria morbidity in the first year of life in an area where both multidrug-resistant P. falciparum and P. vivax are highly prevalent, data were gathered on all infants attending a referral hospital in Papua, Indonesia, using systematic data forms and hospital computerized records. Additional clinical and laboratory data were prospectively collected from inpatients aged <3 months.

Results . From April 2004 through April 2008, 4976 infants were admitted to the hospital, of whom 1560 (31%) had malaria, with infection equally attributable to P. falciparum and P. vivax. The case-fatality rate was similar for inpatients with P. falciparum malaria (13 [2.2%] of 599 inpatients died) and P. vivax malaria (6 [1.0%] of 603 died; P=.161), whereas severe malarial anemia was more prevalent among those with P. vivax malaria (193 [32%] of 605 vs. 144 [24%] of 601; P=.025). Of the 187 infants aged <3 months, 102 (56%) had P. vivax malaria, and 55 (30%) had P. falciparum malaria. In these young infants, infection with P. vivax was associated with a greater risk of severe anemia (odds ratio, 2.4; 95% confidence interval, 1.03–5.91; P=.041) and severe thrombocytopenia (odds ratio, 3.3; 95% confidence interval, 1.07–10.6; P=.036) compared with those who have P. falciparum infection.

Conclusions . P. vivax malaria is a major cause of morbidity in early infancy. Preventive strategies, early diagnosis, and prompt treatment should be initiated in the perinatal period.