THE PURPOSE OF THIS STUDY was to examine the effects of root preparation using the pulsed Nd:YAG laser, either alone or in combination with manual instrumentation. Study specimens consisting of 18 teeth with associated periodontal pockets from 8 different patients were treated as follows: 5 specimens were root planed with curets followed by laser exposure for 3 minutes using energy settings of 3.0 W at 20 pps; 2 specimens were root planed and then laser treated for 3 minutes using settings of 2.25 W and 20 pps; 4 specimens were treated by laser for 1 minute at settings of 1.75 W and 20 pps followed by root planing; 4 specimens were treated by laser only for 1 minute using settings of 1.75 W and 20 pps; and the remaining 3 teeth served as untreated controls. Both prior to and after completion of the laser and root planing treatments, microbiological samples were obtained from the treated pockets and submitted to a commercial laboratory for analysis of levels of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia. With the exception of two 7-day specimens, all others were extracted immediately post-therapy and processed for SEM examination. All treated specimens, regardless of treatment sequence, exhibited some degree of laser-induced root surface alteration. Notably, laser-treated calculus deposits were free of their characteristic surface layer of microbial plaque. Microbial sampling indicated a post-therapy reduction in levels of all 3 putative microbial pathogens compared to pre-treatment samples and control specimens. However, SEM examination revealed residual deposits of plaque and calculus in all treatment groups. Subgingival use of Nd:YAG lasers appears to be technique sensitive and long-term therapeutic benefits remain to be established.