Aim: The purpose of this study was to evaluate the antimicrobial activity of two experimental pastes containing propolis extract associated with calcium hydroxide against polymicrobial cultures collected from 16 necrotic and fistulae root canals in primary molars of 4-8-year old children. Material and Method: The present study comprised of 16 necrotic and fistulae root canals in primary molars of 4-8-year old children. The agar-well diffusion technique was used to determine the antimicrobial activity of the following pastes: 11.0% ethanolic extract of propolis (EEP) + calcium hydroxide; and 11.0% extract of propolis without ethanol (EP) + calcium hydroxide. EEP, EP and the association of calcium hydroxide and propylene glycol (CHP) was used as the positive control groups, and propylene glycol was used as a negative control group. Friedman and Wilcoxon tests were used to compare the data from the microbial growth inhibition zones (p<0.05). Paste 1 and Paste 2 showed larger growth inhibition zones against microorganisms from root canal samples than CHP (p=0.021 and 0.003, respectively). Paste 2 tended to have larger growth inhibition zones than Paste 1 (p=0.053). The association between propolis and calcium hydroxide was effective in controlling dental infections in vitro.