Chilean primary healthcare practice is analyzed using a Data Envelopment Analysis (DEA) multiple stage approach. We estimate the efficiency level of 259 municipalities nationwide. Since the efficiency score by itself is of limited value for decision making, we use a multivariate tool to help explain the effect of relevant factors. First, we use a cluster analysis to homogenize the units under study. Second, we use DEA to estimate the efficiency levels, which varies from 61% to 71% for urban municipalities, and from 51% to 56% in rural ones. Third, we use bootstrap to estimate confidence intervals for the efficiency scores, and a Biplot method to identify adequate variables to include in the Tobit Model, which is our last stage. We identify six factors associated with rural municipalities' operational efficiency, and two with urban ones. Knowing the efficiency level of municipalities can help determine ways to improve their efficiency.