The aim of this study was to evaluate the effect of subgingival irrigation with propolis extract by clinical and microbiological parameters. Twenty patients diagnosed with chronic periodontitis presenting three non-adjacent teeth with deep pockets were selected. After scaling and root planing, the selected periodontal sites were submitted to one of the following treatments: irrigation with a hydro alcoholic solution of propolis extract twice/week for two weeks (group A); irrigation with a placebo twice/week for two weeks (group B); or no additional treatment (C). Subgingival plaque sampling and scaling and root planing were performed two weeks after clinical data recording. Two weeks later irrigation procedures were started (Baseline). Microbiological and clinical data were collected at baseline, and after 4, 6 and 24 weeks. A decrease in total viable counts of anaerobic bacteria (p=0.007), an increase in the proportion of sites with low levels (= 103 cfu/mL) of Porphyromonas gingivalis (p=0.005), and a decrease in the number of sites with detectable presence of yeasts (p=0.000) were observed in group A sites when compared to group B and C sites. Propolis treatment did not lead to an increase in organisms such as coagulase positive Staphylococci and Pseudomonas spp. 24 weeks after treatment there was an increased proportion of sites showing probing depth (PD) = 3 mm in Group A sites. Subgingival irrigation with propolis extract as an adjuvant to periodontal treatment was more effective than conventional treatment both by clinical and microbiological parameters. Keywords: propolis, bacteria, periodontitis, irrigation, periodontal pocket