The article presents the methodology used in the Baseline Study that evaluated the effectiveness of the Family Health Strategy as compared to traditional primary health care units. The study included 41 municipalities with more than 100 thousand inhabitants each, 21 from the South and 20 from the Northeast of Brazil. As the principal dependent variable and underlying premise for sampling in the Baseline Study, the effectiveness of program activities in the primary care units was analyzed in the population within the respective coverage areas, using an epidemiological survey. The health care model in the primary care units was the principal independent variable. Its effect on program activities was controlled according to geopolitical region, metropolitan area, and population size in the municipalities. Coverage of the activities was characterized according to socioeconomic, demographic, and health-related factors. The use of comparison groups, multiple-stage samples, standardized measures, adjustment for geographic and socio-demographic characteristics, and well-defined criteria for judging the findings are contributions by the methodology employed here for designing future studies to evaluate primary health care.