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Eight patients with moderate Periodontitis volunteered to participate in a study to assess the effect of subgingival 2% chlorhexidine irrigation, with and without scaling and root planing, on clinical parameters and the level of Bacteroides gingivalis in periodontal pockets. Each quadrant was required to have at least one site with a probing depth of 6 mm or greater and bleeding on probing. The patients were treated following a randomized four quadrant design: one quadrant received no treatment; a second quadrant received scaling and root planing only; a third quadrant received Chlorhexidine irrigation only; the fourth quadrant received scaling and root planing, plus Chlorhexidine irrigation. Sites to receive Chlorhexidine were irrigated at 0, 1, 2, and 3 weeks. Clinical and microbiological indices were measured and recorded at 0, 5, 7, 11, and 15 weeks.The clinical parameters measured included; Plaque Index (PI), Gingival Index (GI), probing depth (PD), Bleeding Tendency (BT), and attachment level (AL). The attachment level was measured using an occlusal stint as a fixed reference point. The level of Bacteroides gingivalis was measured by labeling the plaque sample with a polyclonal fluorescent antibody. The plaque smear was then read using a fluorescent microscope at 1000 magnification. The Spearman Rank‐Order Correlation was used to determine the relationship between parameters at baseline. The effects of the treatment groups were compared using the NeumanKeuls Multiple Comparison Technique.The results showed that a positive correlation existed between B. gingivalis (rs = 0.68) and Bleeding Tendency and between P1I (rs = 0.77) and GI. In addition, a positive correlation existed between PI (rs = 0.62) and BT, as well as GI (rs = 0.67) and BT. The correlation between P1I and PD was (rs= 0.51), and between GI and PD (rs= 0.59). All parameters, at most time periods, were significantly reduced (P < 0.05) in the root planing group. PlI was significantly reduced only at 5 weeks, and the level of B. gingivalis was significantly reduced only through 7 weeks. Chlorhexidine irrigation alone significantly reduced all parameters from baseline (P < 0.05). The reduction of B. gingivalis extended through the 11‐week period. Scaling and root planing plus irrigation reduced the B. gingivalis significantly more than irrigation (P < 0.01) or root planing (P < 0.01) alone. This reduction occurred through the 11‐week‐period but did not extend to the fifteenth week. The combined therapies resulted in significantly greater attachment gain (P < 0.05) at 5 and 7 weeks than root planing alone.In conclusion, meticulous root planing was an effective treatment in deep pockets through the 7‐week period. Irrigation with 2% Chlorhexidine alone was nearly as effective as root planing. Attachment levels were further enhanced and the level of B. gingivalis was further reduced by the addition of 2% Chlorhexidine to scaling and root planing.