Background In endemic regions, the age distribution of malaria varies according to the infecting Plasmodium species. We aimed to delineate the pattern of malaria-related hospitalization from birth in Timika, Papua-an area co-endemic for P. falciparum and P. vivax Methods Between April 2004 and December 2013, infants born at Mitra Masyarakat Hospital, or presenting within the first 7 days of life, were enrolled retrospectively into a cohort study and followed passively using routinely-collected hospital surveillance data. Outcomes were stratified by the presence or absence of Plasmodium parasitemia and included representation to hospital, requirement for hospital admission and death. Results Overall, 11,408 infants were enrolled into the cohort. Median follow-up was 4.3 (maximum 9.7) years. In total, 7,847 (68.9%) infants made 90,766 representations to hospital, 18,105 (19.9%) of which were associated with Plasmodium parasitemia. The incidence of representations with malaria during the first year of life was 213 per 1,000 person-years (py) for P. vivax and 79 per 1,000py for P. falciparum (Incidence Rate Ratio (IRR) = 2.69, 95% Confidence Interval (95%CI): 2.48-2.92). After the age of 5 years, the incidence of P. vivax had fallen to 77/1,000py and the incidence of P. falciparum had risen to 95/1,000py (IRR = 0.80, 95%CI: 0.73-0.88). Overall, 79.7% (14,431/18,105) of malaria representations were recurrences rather than initial infections. Malaria accounted for 31.7% (2,126/3,120) of all hospital