Information on intraoral distribution of putative periodontal pathogens might be essential for controlling different forms of periodontal disease. Colonization may be either promoted or impeded by other bacteria competing in the subgingival ecosystem. In recent investigations microbial associations between dental organisms have been determined in a multitude of subgingival plaque samples within multiple patients and described by odds ratios, in most circumstances without taking into account the correlated structure of the observations within a single individual. The present investigation had 3 major objectives: (i) to describe the intraoral distribution of some facultatively anaerobic, Gram-negative rods, i.e. Actinobacillus actinomycetemcomitans, Eikenella corrodens-like organisms and Capnocytophaga spp., in a multitude of subgingival and extracrevicular samples of 10 adult subjects with A. actinomycetemcomitans-associated periodontitis; (ii) to analyse possible inconsistencies of microbial associations between these periodontal organisms; and (iii) to determine factors increasing the likelihood of isolating these bacteria in a given subgingival site by employing Generalized Estimation Equation (GEE) methods. Clinical examinations were carried out at 6 sites of every tooth present. In each subject, 13 extracrevicular (2 cheek mucosa, 3 tongue, 4 gingival, 2 tonsillar samples, 1 palatinal, 1 saliva sample) and between 22 and 44 subgingival samples from deepest sites of every tooth present (n = 296) were selectively cultivated for A. actinomycetemcomitans, E. corrodens and Capnocytophaga spp. In extracrevicular material, A. actinomycetemcomitans, Capnocytophaga spp. and E. corrodens were isolated in 9, 10 and 6 patients, and from 65, 82 and 15% samples, respectively. The organisms were recovered from 51, 62 and 27% subgingival plaque samples, respectively. Heterogeneity tests did not reveal significant inconsistencies of microbial associations between bacteria in subgingival plaque. Mantel-Haenszel's odds ratios ranged between 2.0 for A. actinomycetemcomitans and Capnocytophaga spp. and 18.7 for Capnocytophaga spp. and E. corrodens. An exchangeable working dependence structure was employed in the GEE approach. The odds of isolating A. actinomycetemcomitans was increased by factor 3.7 in 4-6 mm deep pockets, and 9.5 in > or = 7 mm deep pockets. The odds of presence of E. corrodens was increased by factor 10.8 in the case of presence of Capnocytophaga spp. and 2.1 in the case of presence of A. actinomycetemcomitans. Capnocytophaga spp. were associated with bleeding on probing and molar sites. Presence of E. corrodens was associated with clinical attachment loss but not periodontal probing depth. Results of the present study indicated an association of A. actinomycetemcomitans with periodontal pathology. Whereas this organism and Capnocytophagae were widely distributed in extracrevicular ecosystems of the mouth, E. corrodens only occasionally appeared in saliva or on mucous membranes of the oral cavity. In general, GEE methods seem to allow to determine factors associated with the presence of periodontal organisms in a multivariate approach and considering the correlated structure of the data.