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Background In Brazil, the incidence of dengue greatly increased in the last two decades and there are several factors impeding the control of the disease. The present study focused on describing the space-time evolution of dengue in Brazil from 2001 to 2012 and analyzing the relationship of the reported cases with socio-demographic and environmental factors. Methods The analytic units used in the preparation of thematic maps were municipalities. Statistical tests and multilevel regression models were used to evaluate the association between dengue incidence and the following factors: climate, diagnostic period, demographic density, percentage of people living in rural areas, Gross Domestic Product, Gini index, percentage of garbage collection and the rate of households with a sewage network. Results The largest accumulation of dengue cases in Brazil was concentrated on the Atlantic coast and in the interior part of Sao Paulo State. The risk of dengue in subtropical and tropical climates was 1.20–11 times lower than that observed in semi-arid climates. In 2009–2010 and 2011–2012, the risks were ten and six times higher than in 2003–2004, respectively. Conclusion Dengue is a common infection in the Brazilian population, with the largest accumulation of dengue cases concentrated on the Atlantic coast and in the interior area of Sao Paulo State. The high dengue rates observed in the Brazilian coastal region suggest that the cases imported from neighboring countries contribute to the spread of the disease in the country. Our results suggest that several socio-demographic and environmental factors resulted in the increase of dengue in the country over time. This is likely applicable to the occurrence of other arboviruses like Zika and chikungunya. To reverse the situation, Brazil must implement effective public policies that offer basic services such as garbage collection and sanitation networks as well as reduce vector populations.