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Background: Primaquine (PQ) is the first choice hypnozoiticidal drug, avoiding relapses of Plasmodium vivax, an essential tool for the control and elimination of malaria. However, the difficulty in diagnosing deficiency of glucose-6-phosphate dehydrogenase (G6PD) in the field areas prevents the safe use of PQ, since it is hematotoxic in deficient individuals, which can lead to severe hemolysis. This study aims to estimate the prevalence of G6PD deficiency in endemic areas for malaria in Brazilian Amazon. Materials and Methods: A cross sectional survey was conducted in the in 43 municipalities in the states of Amazonas, Pará, Roraima and Rondônia. Male individuals were selected from the urban and peri-urban areas of these municipalities. A qualitative rapid fluorescent spot test (R & D DIAGNOSTICS®) was performed using whole blood obtained by digital puncture in EDTA microtubes. The point and interval estimates of the prevalence of G6PD deficiency will be calculated with representativeness for each of the states included in the study. Results: For this study 9.160 individuals were included and 4.9% (448/9.160) were G6PD deficient. In the states of Amazonas, Rondônia and Roraima, all with the survey already concluded, the prevalence was of 4.0%, 5.4% and 4.2%, respectively. The partial result in the state of Pará, with 1732 samples collected, the prevalence was of 6.5%. Conclusions: Our results indicate that an important portion of the population living in endemic áreas of Brazilian Amazon is under risk of hemolysis induced by PQ. The use of rapid tests previously the treatment is essential to ensure the safety of G6PD deficient individuals and should be considered in the implementation of elimination strategies based on PQ use.