Malaria epidemics occur annually in various municipalities (counties) in the Brazilian Amazon. However, health services do not systematically adopt tools to detect and promptly control these events. This article aimed to characterize malaria epidemics in the Brazilian Amazon Region based on their duration, the Plasmodium species involved, and the population's degree of vulnerability. An automatic malaria incidence monitoring system based on quartiles was assessed for prompt identification of malaria epidemics. In 2010, epidemics were identified in 338 (41.9%) of the counties in the Brazilian Amazon. P. falciparum and P. vivax epidemics were detected, both singly and in combination. Epidemics lasted from 1 to 4 months in 58.3% of the counties, 5 to 8 months in 34.5%, and 9 to 12 months in 17.4%. Systematic monitoring of malaria incidence could contribute to early detection of epidemics and improve the effectiveness of control measures.