The purpose of this study was to evaluate the microbiological effects of repeated subgingival irrigation of deep periodontal pockets as a single measure of treatment as well as combined with mechanical debridement, and to study the concomitant radiographical changes of the alveolar bone. 2-3 interproximal sites per jaw quadrant in 10 patients showing a probing depth of greater than or equal to 6 mm and bleeding on pocket probing were selected for the study. The pockets in the various quadrants were randomly assigned to professionally performed subgingival irrigation with 0.2% chlorhexidine gluconate, 3% hydrogen peroxide or saline or to non-irrigation. During a first phase of treatment, the pockets were periodically irrigated (every 2nd-3rd day during weeks 1-2 and 5-6) and no subgingival mechanical debridement was performed. During a second phase, subgingival scaling and root planning were carried out with adjunctive subgingival irrigation of the pockets. During the entire trial, the patients' plaque control was carefully supervised. Sampling of the subgingival microflora was performed before and after the first and second treatment phases and 3 months after the termination of the active treatment. Dark-field assessment and cultivation of the bacterial samples were performed. The radiographical examination was carried out at the start of each treatment phase and 3 months after the termination of phase II and the radiographs were analysed by the use of a subtraction technique. The results demonstrated that periodic subgingival antimicrobial irrigation per se had only limited and transient effects on the subgingival microflora.(ABSTRACT TRUNCATED AT 250 WORDS)