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Immunization is known to be one of the most successful and cost-effective health interventions, resulting in the eradication and control of various diseases in the world. However, Brazil has experienced a worrisome drop in vaccination coverage, associated with the resurgence of various previously controlled or eradicated diseases. This study thus conducted a situational diagnosis weighing Brazil's different regions and time trends in vaccination coverage in order to identify areas with reduction in vaccination coverage for BCG, poliomyelitis, and MMR. This ecological study collected data on the number of children up to one year of age who had been vaccinated with these three vaccines from 2006 to 2016, according to municipality (county). Data were obtained from the Brazilian Health Informatics Department. A spatial scan was performed, analyzing spatial variations in the time trends for vaccination coverage. Downward trends were seen in the number of immunizations in Brazil, with reductions of 0.9%, 1.3%, and 2.7% per year for BCG, poliomyelitis, and MMR, respectively. Significant decreases were also seen in all five major geographic regions with time trends in the reduction of vaccination coverage. The study evidenced an important reduction in vaccination coverage in recent years, with major heterogeneity between municipalities. Thus, focused attention and strategic planning in keeping with each local area's characteristics are necessary to address both the reduction of vaccination coverage and the resurgence of vaccine-preventable diseases in Brazil.