Background: The effect of timing of exposure to first Plasmodium falciparum infections during early childhood on the induction of innate and adaptive cytokine responses and their contribution to the development of clinical malaria immunity is not well established. Methods: As part of a double-blind randomized placebo-controlled trial in Mozambique using monthly chemoprophylaxis with sulfadoxine-pyrimethamine plus artesunate to selectively control timing of malaria exposure during infancy, peripheral blood mononuclear cells collected at ages 2.5, 5.5, 10.5, 15 and 24 months were stimulated ex vivo with parasite schizont and erythrocyte lysates. Cytokine mRNA expressed in cell pellets and proteins secreted in supernatants were quantified by real time quantitative PCR and multiplex flow cytometry, respectively. Children were followed up for clinical malaria from birth until 4 years of age. Results: Higher pro-inflammatory (IL-1, IL-6, TNF) and regulatory (IL-10) cytokine concentrations during the second year of life were associated with reduced incidence of clinical malaria up to 4 years of age, adjusting by chemoprophylaxis and prior malaria exposure. Significantly lower concentrations of antigen-specific TH1 (IL-2, IL-12, IFN-) and TH2 (IL-4, IL-5) cytokines by 2 years of age were measured in children under chemoprophylaxis compared to children receiving placebo (p<0.03). Conclusions: Selective chemoprophylaxis altering early natural exposure to malaria blood stage antigens during infancy had a significant effect on TH lymphocyte cytokine production more than one year later. Importantly, a balanced pro-inflammatory and anti-inflammatory cytokine signature probably by innate cells around age 2 years was associated with protective clinical immunity during childhood.