The purpose of this examiner-blind study was threefold: to compare the microbial counts obtained by two different techniques for assessing bacterial motility, to assess the inter-rater reliability of these two techniques and to evaluate the effect of a water irrigating device (Water Pik) on bacterial motility at 3- and 6-mm probing depths. Subgingival plaque samples were taken from 10 healthy patients having at least two sites that probed greater than 6 mm, (one control, one experimental). Half of the patients were sampled at 3 mm, the other half at 6 mm, both at baseline (Day 0) and at Day 21. Two slides were prepared from each plaque sample, one for dark-field evaluation and one stained with a simplified silver-plating technique for flagella. All slides were read simultaneously by 3 observers, and the per cent motility calculated for spirochetes, motiles and all others. Strong positive inter-rater reliability correlations ranging from r = 0.95 to r = 0.99 were found for both the dark-field and flagella staining techniques. Spirochete counts obtained by both techniques were highly correlated (r = 0.91), whereas counts for motiles resulted in negative correlations between the techniques. Dark-field counts were consistently higher than the flagella stain counts for motile rods. Spirochetes were reduced, but not significantly, after irrigation of both 3-mm and 6-mm sites. Bacterial motility can be evaluated by both dark-field and flagella-staining techniques with a high degree of inter-rater reliability.