The aim of this study was to identify different profiles in the AIDS epidemic in Brazil by relating them to the health sector's organization, situations involving increased risk of infection, and the degree of implementation of the response by health services. The Brazilian municipalities (counties) were grouped according to the magnitude of the epidemic and its trends from 2002 and 2006, and were then studied using indicators obtained from secondary databases. Municipalities with large epidemics (39%) displayed more situations associated with risk of infection, and those with an upward trend in incidence (11.5%) showed a lower degree of response. Cities with large epidemics but with downward or stable trends had 68.6% of all the anonymous testing centers and 75.8% of the outpatient clinics, and performed 81.4% of all the HIV antibody tests in the health system. Preventive measures in schools and primary health services showed low coverage rates. Differences were observed between geographic regions. Inequalities in the degree of implementation of the response to HIV may contribute to different profiles in the epidemic around the country.