Aim: The aim of this study was to compare the microbial profile of subgingival sites in Periodontitis (Pd) patients and healthy ones. Methods: Eighteen patients with Pd and 18 gender-matched healthy controls were selected. Subgingival samples were collected from three types of sites: 1) healthy site of healthy subjects (probing pocket depth (PPD) ≤ 3mm, CG), 2) healthy site of Pd patients (PPD ≤ 3mm, PG-C) and 3) diseased site (PPD > 3mm) of the same Pd patients (PG-T). All sites were subjected to microbial analysis for the detection of 40 bacterial species by the "Checkerboard DNA-DNA hybridization" technique. Results: It was observed a great diversity of bacteria in all patients evaluated. The sites from the Pd groups (PG-T and PG-C) showed a higher overall count of the studied bacteria than those of the CG group, especially from Green, Orange, and Red complexes. Also, PG-T showed a higher prevalence of Red complex bacteria than CG. Individual pathogens, such as Porphyromonas gingivalis, Treponema denticola and Treponema socranskii were detected in higher levels and/or prevalence in Pd than in control patients. However, it was not observed any difference between PG-T and PG-C. Conclusion: Pd patients showed higher prevalence and counts of some putative periodontal bacteria, especially from the red complex, than control ones, regardless of the severity of their sites.