Marginal periodontitis in humans is characterized by phases of clinical disease progression, which are interspersed between periods of quiescence. The purpose of the present study was to compare subgingival bacterial populations from periodontal sites undergoing episodic probing attachment loss with bacterial populations from non-progressing lesions. Probing depth and attachment levels were measured in 10 adult patients at baseline, and every 30 days thereafter for 10 months. Pairs of corresponding contralateral sites were identified where one site had lost probing attachment within the previous month (P) and the other site had not (C). Subgingival bacterial samples were obtained from these sites and analyzed using darkfield microscopy. Motile forms, spirochetes, curved and straight rods, filaments, coccoid cells, fusiforms, and the total number of bacteria were assessed. The results showed that median pocket depth and attachment change were statistically significantly greater in P-sites as compared to C-sites. There was no significant difference in bacterial populations between P- and C-sites (p greater than 0.15). Motile forms, spirochetes, and total number of bacteria were positively correlated with pocket depth in P-sites, while in C-sites the same was true only for curved rods. These results suggest that darkfield microscopy of subgingival bacteria in humans represents primarily pocket depth.