Two rapid methods of identifying bacteria associated with periodontal disease were investigated to determine their diagnostic usefulness in longitudinal or epidemiologic studies. Three nonmotile organisms were identified by fluorescent antibody stains (FA) while percentages of motile bacteria were assessed by counting all spirochetes, flagellated and nonflagellated organisms stained with a simplified silver-plating stain for flagella. Relationships between disease activity and these bacteria from subgingival plaque samples taken at 18 individual sites (12 diseased, 6 healthy) were determined by correlating the quantity of detectable bacteria with the Gingival Index (GI), Plaque Index (PLI) and probing depth (PD). The highest correlations found with the FA stains were between Bacteroides gingivalis and probing depth (rs = 0.85), GI (rs = 0.80) and PLI (rs = 0.80). Bacteroides melaninogenicus and/or Bacteroides intermedius also correlated well with the GI (rs = 0.66), PLI (rs = 0.64), and PD (rs = 0.59), but to a lesser degree than B. gingivalis. Flagella stains showed that spirochetes correlated highly with PD (rs = 0.82), as did the total motile group with PLI (rs = 0.82). Motile bacteria alone were only moderately associated with the clinical parameters measured. The results of this investigation suggest that FA- and flagella-staining methods can be valuable screening tools for the detection of bacterial species and motile organisms in longitudinal or epidemiologic studies.