The objective of this study was to examine potential benefits of using laser therapy for secular decontamination in conjunction with scaling and root planing in the treatment of chronic periodontitis. The study was performed on 173 teeth in 14 patients in a split-mouth design, one side received scaling and root planing followed by laser therapy using a carbon dioxide (CO2) laser with an ablative handpiece (test group); the contralateral side received scaling and root planing without laser (control group). Clinical and laboratory parameters were evaluated prior to treatment and at 3 and 6 months following therapy; clinical measurements were performed by two blinded examiners. The clinical parameters included measurement of gingival recession (REC), bleeding on probing (BOP), clinical attachment level (CAL), pocket depth (PD), furcation involvement (FUR), and tooth mobility (MOB). Laboratory testing to determine the levels of periodontal pathogens was performed using PCR techniques. The results of the study revealed statistically significant differences in clinical and laboratory parameters at 3 and 6 months after therapy for both test and control groups, but no significant difference was observed between the two groups. However, sites receiving laser therapy tended to show a greater decrease in probing depths, gain in clinical attachment level, and reduced bacterial levels. In conclusion, the overall results of the study suggest a potential benefit of using laser therapy in conjunction with scaling and root planing for the treatment of chronic periodontitis.