Context: Antimicrobial efficacy of subgingival chlorhexidine (CHX) application using two different vehicles of delivery. Aims: The aim was to evaluate the efficacy of CHX varnish and gel as an adjunct to scaling and root planing (SRP) in reducing microbial count within moderate to deep periodontal pockets. Settings and Design: Experimental parallel mouth study. Subjects and Methods: A total of 30 subjects between the age groups 25 and 55 years having moderate to severe periodontitis, with pocket depth ≥ 5 mm were selected for the study. The selected patients were randomized into three groups of 10 each. Subjects in Group 1 received SRP followed by subgingival application of CHX varnish, subjects in Group 2 received SRP followed by subgingival application of CHX gel, subjects in Group 3 received SRP alone. Subgingival plaque samples were collected to estimate mean motile and nonmotile microbial counts using dark field microscopy at baseline, 1 week, 1 month, and 3 months. Results: After 3 months, there was statistically significant reduction in nonmotile microbial count in all the three groups. Motile microbial count was significantly reduced in all the three groups till 1 month from baseline. Only subjects in Group 1 who received subgingival CHXvarnish after SRP showed a significant reduction in motile microbial count till 3 months from baseline. Conclusions: Subgingival application of highly concentrated CHX varnish following SRP is beneficial in reducing microbial count in moderate to deep periodontal pockets.