To explore the feasibility of field sites for malaria vaccine trials, we conducted a prospective study of clinical malaria incidence during two consecutive transmission seasons in children and young adults living in two areas of Mali with different entomologic inoculation rates (EIRs). Approximately 200 subjects (3 months to 2 years of age) were enrolled per site and followed weekly. Malaria smears were performed monthly in all participants and when symptoms or signs of malaria were present. In Sotuba (annual EIR < 15 infective bites per person), the incidence of clinical malaria was comparable across all age groups but varied significantly between the 2 years. In contrast, in Donéguébougou (annual EIR > 100 infective bites per person), incidence rates decreased significantly with increasing age but remained stable between years. Our results suggest that, although the age distribution of clinical malaria depends on transmission intensity, the total burden of disease may be similar or higher in settings of low transmission.