The effect of mechanical supragingival plaque control on the composition of the subgingival microflora in untreated 4-6 mm deep periodontal pockets was investigated. 13 subjects with chronic periodontitis were recruited for the study. Periodontally-diseased sites were subjected to professional plaque control 3 x weekly for a period of 3 weeks. Contralateral sites received no prophylaxis and served as controls. No instructions in oral hygiene procedures were given to the patients who maintained their habitual oral hygiene regime during the observation period. Clinical examination and darkfield microscopic analysis of bacterial samples were performed every week. The PlI scores for the experimental sites were reduced markedly, while those for the control sites remained stable throughout the observation period. No changes in the other clinical parameters were detected during the study. The composition of the subgingival microflora at the control sites did not change during the experimental period. In contrast, at the test sites, the proportion of spirochetes+motile rods decreased continuously. This decrease reached statistical significance at the end of the experiment. The results indicate that at periodontally diseased sites with an established subgingival ecosystem, supragingival plaque removal may influence the composition of the subgingival microflora.