AbstractCharacterization of the parasite reservoir is required to improve malaria control. Asymptomatic patients with subpatent parasitemia have been identified in Gabon, but the prevalence of such infections among febrile subjects is unclear. We assessed the prevalence of submicroscopic Plasmodium falciparum infections on an island (Port-Gentil), and in urban (Libreville), semiurban (Melen), and rural (Oyem) settings in Gabon. Blood samples (N = 310) from febrile patients were tested for malaria parasites by quantitative nucleic acid sequence-based amplification (QT-NASBA). Parasites were detected in 55.8% (173/310) of samples by microscopy and in 66.4% (206/310) of samples by 18S rRNA QT-NASBA. The proportion of submicroscopic infections differed considerably between sites. Gametocytes were found in 1% (3/310) of the individuals by microscopy and in 32% (99/310) by Pfs25 mRNA QT-NASBA. Thus, submicroscopic parasitemia is frequent in febrile patients, and the detection of this condition is important, to improve disease control.