The number of dengue epidemics in Brazil has increased dramatically in the last 15 years. In this study, we analysed the seasonal patterns in the incidence of hospitalisations due to dengue across the different states of Brazil and compared these with the corresponding climatic patterns. We discovered that the seasonality of dengue hospitalisations in Brazil has a clear zonal gradient, characterised by the progression of primary peaks from West to East during the first half of the year, which may be associated with the increased vapour pressure and rainfall during this period, leading to increased mosquito abundance and activity. We also found that the proportion of children among hospitalised individuals was especially high during the peak outbreaks in 2007/2008 and 2010. This may be due to the emergence and spread of the new DENV-2 Southeast Asian genotype lineage II from 2007, which has probably arrived from the Caribbean and may have caused an increase in incidence and severity of the disease, particularly among children. Our findings may allow health systems to improve control interventions and contribute to reducing dengue morbidity and mortality by using integrated vector control in conjunction with early diagnosis and prompt supportive care.