BACKGROUND The objective of this study was to evaluate clinically the effectiveness of a chlorhexidine gluconate chip in sites still showing signs of disease during periodontal maintenance therapy. METHODS Forty-two maintenance non-smoking patients (previously treated with non-surgical scaling and root planing [SRP]), presenting at least one probing depth (PD) of 5 to 8 mm, and bleeding on probing (BOP) at single-rooted teeth were assigned randomly to two groups: treated with a chlorhexidine gluconate chip (CHIP group) and treated with SRP (SRP group). Patients were assessed for plaque index, gingival index, BOP, PD, clinical attachment level (CAL), and gingival recession at baseline, 6 weeks, and 3 and 6 months. RESULTS Both treatments resulted in improvements in all parameters evaluated. After 6 months, a reduction in PD of 2.64 +/- 0.02 mm and 2.12 +/- 0.02 mm was observed for CHIP and SRP groups, respectively (P >0.05). The observed gain in CAL was 2.19 +/- 0.87 mm and 2.07 +/- 1.53 mm for CHIP and SRP groups, respectively (P >0.05). In deep pockets, PD reduction was 3.60 +/- 0.70 mm for CHIP group and 2.83 +/- 0.62 mm for SRP group (P = 0.01). CONCLUSIONS Both treatments were equally effective in periodontal health reestablishment in inflamed single-root sites of maintenance patients. However, for deep pockets, the chlorhexidine gluconate chip was more effective than SRP in reducing PD.