This study was designed to investigate the effect of conventional oral hygiene (n = 116 subjects) versus a salt and peroxide oral hygiene regimen (n = 115 subjects) on subgingival microorganisms. Subgingival plaque for microscopic evaluation was obtained from eight index tooth sites in each of 231 adult subjects. Microbial forms were microscopically identified at baseline, 8, 16, and 24 months. For both oral hygiene groups, cocci were increased (P less than 0.05) and motile rods were decreased (P less than 0.05) at 8 months and returned to baseline by 16 months. Spirochetes were decreased (P less than 0.05) and remained low through 24 months in both oral hygiene groups. The frequency of agreement between clinical (bleeding) and microbial (greater than or equal to 15% spirochetes or motile rods or greater than or equal to 20% spirochetes + motile rods) criteria for instrumentation was 59.8%. It was also found that fewer total instrumentations for test subjects were observed when microbiological criteria were used as compared with clinical criteria. The greater number of instrumentations based on clinical criteria was highly significant (P less than or equal to 0.001). A significant change in microbial signs associated with peridontal disease may be obtained with either a conventional oral hygiene or a salt and peroxide oral hygiene home care regimen.