The aims of this study were to compare the prevalence of suspected periodontal pathogens in subgingival plaque from 29 HIV seropositive and 27 control subjects and to determine the association of these bacteria with periodontal destruction. Subgingival plaque was collected from the mesiobuccal sites of all teeth, except 3rd molars. Bacteria were identified and enumerated using non-isotopic whole chromosomal DNA probes and a colony lift method. At baseline, HIV seropositive subjects had significantly higher mean % of Porphyromonas gingivalis than control subjects. This difference could be attributed to a subgroup of HIV seropositive subjects with widespread attachment loss. No correlations were observed between the mean %s of DNA probe species and mean attachment loss, CD4 and CD8 T lymphocyte counts or CD4: CD8 ratio. No significant microbiological differences were detected between active and control sites in HIV seropositive subjects on a longitudinal basis. There appeared to be an inverse relationship between the mean %s of P. gingivalis and V. parvula, with respect to progression of HIV infection. The ability of microbiological parameters to predict site-specific breakdown in HIV seropositive subjects requires further investigation.