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Background  The epidemiological surveillance of malaria is a necessary intervention for eliminating the disease from the planet. The international border zones of the Amazon continue to be highly vulnerable to malaria since population mobility impedes elimination. Although in the past few years, cases of malaria have had an essential reduction in Brazil, this trend was not confirmed in municipalities along the border. This study aimed to establish the epidemiology of the disease during the last 13 years in Oiapoque, a Brazilian municipality at the international border with French Guiana, an overseas department, to develop strategies for the control/elimination of malaria in these areas.    Results  Data collected from 2003 to 2015 from the Malaria Epidemiological Surveillance System was used. It was found that, despite the important reduction in cases (68.1%), the annual parasite index remained a high epidemiological risk. The disease is seasonal in that the period of highest transmission occurs between September and December. Between 2003 and 2015, eight outbreaks were identified, with one of these lasting 15 months between August 2006 and October 2007. There were changes in the epidemiological profile, with imported cases representing 67.7% of cases from 2003 to 2007 and representing 32.9% of cases from 2008 to 2015 ( p  < 0.01). The greatest number of cases was among Brazilians coming from the artisanal gold mines of French Guiana. There were also changes in the profile of autochthonous malaria with an increase in urban cases from 14.3% in 2003 to 32.3% in 2015 ( p  < 0 .01). The burden of malaria in indigenous areas was also very high (67.3% in rural areas) in 2015. There were changes in the parasite species profile with a significant decrease of cases of  Plasmodium falciparum  ( p  = 0.01). Children under 15 years old, representing 9.7% of cases at the onset of the study, accounted for 34.2% of case notifications ( p  < 0.01) in 2015. Also, 74% of cases in 2003 and 55.9% in 2015 ( p  < 0.01) were among men.    Conclusions  The fragility of local health services in cross-border areas continues to be an obstacle for malaria elimination.    Electronic supplementary material  The online version of this article (10.1186/s41182-019-0150-0) contains supplementary material, which is available to authorized users.

Complex malaria epidemiology in an international border area between Brazil and French Guiana: challenges for elimination