BACKGROUND The present clinical trial was designed to investigate the effectiveness of subgingivally delivered satranidazole (SZ) gel as an adjunct to scaling and root planing (SRP) in the treatment of smokers with chronic periodontitis. METHODS Sixty smoker subjects with probing depth (PD) ≥ 5 mm were selected. Thirty subjects each were randomly assigned to SRP + placebo and SRP + SZ. SZ or placebo (0.1 mL) was injected into the pocket using a syringe with a blunt cannula. The clinical outcomes evaluated were plaque index (PI), gingival index (GI), clinical attachment level (CAL) and PD at baseline, 1 month, 3 months and 6 months. RESULTS At 6 months, SRP + SZ resulted in greater mean reduction (3.05 mm) in PD as compared to SRP + placebo (1.97 mm; p < 0.05) and also a greater mean CAL gain (2.89 mm) in SRP + SZ as compared to SRP + placebo (1.88 mm; p < 0.05). CONCLUSIONS When compared to the placebo, the adjunctive use of 3% SZ resulted in significant improvement in clinical outcome in the treatment of chronic periodontitis among smokers.