The aim of this article is to examine regional differences in mortality associated with influenza from 2006 to 2010 in Brazil. Syndromic surveillance, which includes deaths from pneumonia and influenza recorded in the Mortality Information System, only showed an increase in mortality during the pandemic in the South, Southeast, and Central, regions. In these regions, especially in the South, this increase occurred from July to September 2009. A review of deaths from confirmed influenza cases reported to the Information System for Notifiable Diseases showed different temporal patterns in the South/Southeast and the North/Northeast, with an increase from July to November 2009 for all regions and another peak, only for the latter, in March 2010, before the vaccination campaign. The results show regional differences in the intensity and temporal distribution of pandemic influenza and highlight the need for specific surveillance tools and control strategies for regions of the country.