This study investigated the effects of sodium bicarbonate and hydrogen peroxide on the microbial flora of 4 to 7 mm periodontal pockets. Four selected patients were instructed to brush assigned quadrants daily with a sodium bicarbonate-3% hydrogen peroxide paste utilizing a split-mouth design. The paste was pumped between the teeth and gingiva via sulcular brushing and a Perio Aid. The control sides were treated in the identical manner with fluoridated paste. Probing depths on each patient were taken on Days 1 and 21 and examined under dark-field microscopy. For each sample, morphology and motility of all cells were recorded. The data were analyzed by three factor repeated measures analysis of variance. No statistically significant differences were found between the control and medicament sites at the 0.005 level regarding changes in the microbial flora. Probing depths were reduced during the study. However, similar results were found on both medicament and control sites. It appeared that sodium bicarbonate and hydrogen peroxide have no unusual benefits in reducing the microbial flora of periodontal pockets.