OBJECTIVE This study is intended to verify the correlation among clinical indices of the peri-implant soft tissues, the histological condition and the presence of 3 pathogens commonly associated with peri-implant diseases (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythia). METHODS Four clinical indices, Gingival Index (GI), Sulcus Bleeding Index, GI modified by Mombelli, and Plaque Index modified by Mombelli (mPI) were evaluated around 1 dental implant of each subject (n = 10). Subgingival plaque was collected for bacterial analysis (polymerase chain reaction) and a biopsy of peri-implant soft tissues for histological analysis was harvested. The clinical indices and detected pathogens correlated with a developed histological index (HI). RESULTS There was no statistically significant relationship between the clinical indices (GI, Sulcus Bleeding Index, and GI modified by Mombelli) and the HI, except for the mPI on the central area of lingual aspects (r = 0.85, P = 0.0029). There was a tendency for a positive correlation between the mPI on the central area of buccal aspects and the HI (r = 0.63, P = 0.0544). The counting of lymphocytes and plasmocytes correlated positively with HI, thus suggesting the index reliability. The prevalence of A. actinomycetemcomitans, P. gingivalis, and T. forsythia did not present a significant relationship with the HI. CONCLUSIONS Despite the small number of samples and the poor statistical significance, the mPI seems to be useful for evaluation of inflammatory severity on soft tissue around dental implants as demonstrated by its relationship with the HI. Further studies are necessary to elucidate this subject.