We have previously reported that the Periocheck test offers a rapid, simple periodontal diagnostic tool by detecting peptidase activity specifically attributed to Treponema denticola, Porphyromonas gingivalis, and Bacteroides forsythus. Relationships between the peptidase activity detected by the Periocheck test and clinical measures were investigated. Fifty-seven Periocheck-positive sites selected from 27 patients with adult periodontitis were subjected to scaling and root planing. Two weeks later, a Periocheck test was undertaken in the test sites. Two groups were then determined, one composed of 40 Periocheck-positive sits, and the other consisting of 17 Periocheck-negative sites. All sites were re-examined at 6, 10, 14 and 18 weeks using both the Periocheck test and clinical measures. On week 18, the negative group displayed a significant decrease in probing pocket depth (PD) and a significant attachment level (AL) gain (2.1 and 1.2 mm, respectively), while the positive group showed a slight decrease in PD and AL gain (0.9 and 0.3 mm, respectively). The differences between negative and positive groups in PD and AL became statistically significant by the tenth week. Improvement of gingival index (GI) and bleeding on probing (BOP) was more apparent in the negative group. The detection of intrapocket microbiological status by the Periocheck test preceded the changes in PD, AL, GI, and BOP after periodontal therapy. In conclusion, the Periocheck test may provide a promising chairside monitoring tool for effectively evaluating therapies associated with scaling and root planing.