11 volunteer subjects with advanced chronic periodontitis participated in a 1-year longitudinal clinical and microbiological study. Subgingival plaque was collected at each of 7 visits from 148 pre-selected sites in the left jaw quadrants (test sites) and on the first and last visits, only from 117 sites in the left jaw quadrants (control sites). All sites were examined clinically at each of the 7 visits, and the microbiological markers investigated were the % spirochaetes and % black pigmented Bacteroides species in subgingival plaque. At the completion of the study, the sequential changes in probing attachment level at each site were subjected to regression analysis to determine the direction and extent of attachment change. Possible correlations between attachment change and % spirochaetes or % black-pigmented bacteroides were investigated using both individual sites and individual subjects. No significant differences were observed in either of the microbial variables between test and control sites. Possible correlations between the microbiological markers and attachment changes were investigated at baseline, at the 12-month visit and using the microbial data accumulated over all 7 visits. Significant differences were observed only at the 12-month visit when the % spirochaetes of both test and control sites were significantly lower in subjects showing the greatest improvement in attachment level. Overall, these results indicate that quantification of either spirochaetes or black-pigmented Bacteroides species cannot be used reliably to identify or predict disease-active sites.