THIS STUDY AIMED TO EXAMINE early posttreatment changes in the periodontal microflora. Paper point sampling and conventional bacterial cultivation were used to monitor the effects of surgical and non-surgical periodontal therapy on the detection frequency of Porphyromonas gingivalis, Prevotella intermedia, Actinobacillus actinomycetemcomitans, and Capnocytophaga species in deep periodontal pockets. Ten patients, 5 men and 5 women (mean age 44 years), with advanced periodontal disease were selected from the dental school patient population for the study. A total of 245 teeth in 10 defined areas of the dentition were treated by oral hygiene instruction followed by scaling and root planing alone (121 sites) or with surgical interventions (124 sites). Ninety sites, 47 surgical and 43 non-surgical, with initial pocket depth greater-than-or-equal-to 6 mm were sampled at baseline and 3 months after completion of therapy. Treatment by both procedures resulted in significant clinical improvements as assessed by all clinical parameters used. Baseline results may indicate that the level of P. gingivalis was reduced in the presence of P. intermedia, while A. actinomycetemcomitans seemed to be reduced in the presence of P. gingivalis and/or P. intermedia. Three months after therapy, the detection frequency of P. gingivalis was significantly reduced (P < 0.05) in surgical and non-surgical sites while the reduction for P. intermedia was significant only for surgical sites (P < 0.05). P. intermedia was eliminated from 2/3 of the non-surgical sites that had been positive at baseline, but this reduction did not reach a significant level, and the relative proportion of this organism increased significantly (P < 0.05) in the sites positive after therapy. A. actinomycetemcomitans could not be detected in any of the sampled sites 3 months after therapy. Capnocytophaga species were significantly reduced to the same extent (P < 0.05) following both treatment modalities.