The clinical course of malaria varies between affected individuals and host genetic factors have been shown to influence the outcome of malaria. The role of FOXO3-driven pathway in modulating inflammatory responses, including mediation of distinct functions of regulatory T effector cell populations (Tregs) by the transcription factor FOXO3, has recently been recognized. We aimed to study possible associations of a non-coding polymorphism in intron 2 of the FOXO3A gene (rs12212067T>G) that was shown earlier to modulate the FOXO3 expression and to be associated with the prognosis of distinct inflammatory and infectious diseases. The FOXO3A polymorphism rs12212067T>G was genotyped by direct sequencing in a group of Gabonese children with confirmed Plasmodium falciparum malaria. Severe cases of malaria were compared with asymptomatic/mild cases. The FOXO3A variant rs12212067T>G was associated with the phenotype of severe malaria, but not with asymptomatic/mild malaria (allelic model: OR = 1.54, 95 % CI = 1.15-2.05, P = 0.0028; dominant model: OR = 1.94, 95 % CI = 1.36-2.77, P = 0.0002). The FOXO3A variant rs12212067T>G is associated with increased inflammatory responses to Plasmodium falciparum malaria, indicating a role of the FOXO3-dependent pathway in malaria.