It has become increasingly recognized that groups of microorganisms interact within the subgingival plaque of adult subjects with periodontitis. It is much less clear, however, whether the consortia of microorganisms associated with periodontitis are different in early and more advanced cases of periodontitis. To investigate this point further, subgingival plaque was collected from six sites in 87 adolescents with periodontitis and 73 controls and the samples were analyzed for the detection of 18 microbial species using the DNA-DNA hybridization technique. Actinomyces oris accounted for the highest proportion of the flora and was more predominant among controls. Prevotella nigrescens, Prevotella intermedia, Porphyromonas gingivalis, and Tannerella forsythia were present at higher levels among the subjects with periodontitis. Factor analyses identified one factor characterized by highly positive loadings for T. forsythia, Campylobacter rectus, P. gingivalis, P. intermedia, P. nigrescens, Parvimonas micra, and Treponema denticola, and another factor characterized by highly positive loadings of A. oris, Capnocytophaga ochracea, Eikenella corrodens, Streptococcus intermedius, Selenomonas noxia, Streptococcus oralis, Streptococcus sanguinis, and Veillonella parvula. Aggregatibacter actinomycetemcomitans and Streptococcus mutans did not load on any of the two factors, while Fusobacterium nucleatum loaded on both. These findings confirm the occurrence of clustering of subgingival bacteria according to case status also among young individuals.