The objective of this study was to determine the efficacy of chemical-mechanical procedures of two endodontic protocols for septic content reduction of root canals from primary teeth with pulp necrosis and periradicular lesion. Twenty-four primary root canals with pulp necrosis and periradicular lesion were divided into two treatment groups (n=12): multiple-visit and single-visit protocols. Samples were collected using sterile paper points before and after endodontic cleaning followed by microbiological identification through checkerboard DNA-DNA hybridization. Statistical analysis was performed using Proportion Test for score=0 comparing the findings before and after treatment for each group (Wilcoxon's test) as well as the differences in scores between protocols (Mann-Whitney's test) (p<0.05). Data were expressed as prevalence (presence or absence) and estimate of the average count (x10(5) cells) of each species. Differences in proportions of score=0 prior to treatment were non-significant (p=0.415), demonstrating equivalence between groups. A significant increase in score=0 was detected after treatment for both groups (p<0.0001). Single-visit protocol achieved a significantly greater reduction in mean scoring following endodontic treatment (p=0.024). Both protocols were capable of significantly reducing septic content in root canals of primary teeth with periradicular lesion. Moreover, single-visit protocol showed greater efficacy in reducing endodontic infection.