The aim of this study was to determine whether the Nd:YAG laser energies of 50 and 80 mJ at 10 pulses per second (pps) were capable of improving the clinical parameters associated with periodontal disease. These energy settings were chosen as previous work indicated that higher values would damage root surfaces and that 80 mJ had an in-vitro bactericidal effect. Eighty periodontally affected sites in teeth scheduled for extraction from 11 patients with adult periodontitis were randomly placed in one of the following four treatment groups: 1. laser treatment at 50 mJ, 10 pps for 3 minutes; 2. laser treatment at 80 mJ, 10 pps for 3 minutes; 3. scaling and 4. untreated control. Probing depth, bleeding on probing (BOP), plaque index, gingival index and gingival crevicular fluid (GCF) volume were measured at baseline and week 6. Baseline subgingival microbiological samples were collected, then repeated immediately after treatment and at week 6 to assess the total anaerobic colony forming units (CFU). Only the scaling group showed a significant reduction in pocket depth and BOP (P < 0.001). The microbial samples taken immediately after scaling and laser at 80 mJ and 10 pps treatments showed a significant reduction in total CFU compared with the baseline (P < 0.01), which was sustained only in the scaling group until week 6. Electron microscopy did not reveal any heat damage on the root surfaces. This study demonstrated that application of Nd:YAG laser pulses of 50 mJ and 80 mJ failed to improve the clinical and microbiological parameters of periodontal disease.