OBJECTIVE To analyze Brazilian municipalities according to morbidity and effectiveness of epidemiological inspection control of tuberculosis and AIDS. METHODS Exploratory analysis of two non-hierarchical data clusters of epidemiological inspection data on tuberculosis and AIDS, and operational indicators of the Programa Nacional de Controle de Tuberculose (National Tuberculosis Control Program), from 2001 to 2003. The distribution was stratified in metropolitan areas and priority municipalities, according to the size of the population. The association between morbidity clusters and effectiveness was evaluated by the Chi-square test, with analysis of residues in order to identify significant associations. RESULTS Out of the five morbidity clusters, the concerning epidemiological situation occurs in municipalities with high incidence of Aids, with high or low incidence of tuberculosis, prevailing in the Southeast and South of Brazil and larger cities. Out of the six program effectiveness clusters, moderate and average effectiveness are significantly associated to priority municipalities, in metropolitan areas with more than 80 thousand inhabitants. Clusters with average and poor effectiveness represent 10% of municipalities with elevated treatment drop out and low rates of cure. The "no data" cluster is associated with the very low incidence of tuberculosis and AIDS cluster. CONCLUSIONS The findings reflect inadequacy of inspection concerning the epidemiological reality in Brazil: precarious social factors associated with tuberculosis and AIDS and insufficient effectiveness of the control program.