The oral cavity may act as a reservoir for several pathogens related to systemic infections. Therefore, the purpose of this study was to determine the prevalence and levels of pathogenic bacteria in the subgingival biofilm of chronic periodontitis lesions and healthy periodontal sites using the checkerboard DNA-DNA hybridization technique. 200 samples of subgingival biofilm from sites with periodontitis (probing pocket depth ≥ 4 mm and /or clinical attachment level ≥ 4 mm) and 200 samples from healthy sites of 14 patients with chronic periodontitis, as well as 200 samples from 3 periodontally healthy patients were obtained. The presence and levels of 11 pathogenic bacteria were determined using whole genomic DNA probes and the checkerboard method, computed for each site and then across sites within each subject group. Significance of differences in clinical and microbiological parameters among groups were examinated using the MannWhitney and Wilcoxon sign tests. The predominant species in all 600 samples included Corynebacterium diphtheriae, Enterococcus faecalis, Staphylococcus aureus, Acinetobacter baumannii and Escherichia coli. In general, most of the species were detected in greater prevalence and levels in sites with and without disease from patients with periodontitis in comparison to the periodontally healthy group. In particular, C. diphtheriae, E. coli, E. faecalis, Pseudomonas aeruginosa and S. aureus were significantly more prevalent and detected in higher counts in diseased sites of patients with periodontal disease compared to healthy subjects (p < 0.05). Clinical signs of disease presented a positive correlation with the species A. baumannii, Streptococcus pyogenes, E. coli, S. aureus and P. aeruginosa. In conclusion, "non-oral" pathogenic bacteria are detected in high prevalence and levels in periodontal sites of chronic periodontitis patients.