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Gingival fibromatosis is a rare clinical finding of non-inflammatory gingival overgrowth. Here we present 2 cases of children with gingival fibromatosis and provide a longitudinal analysis of the correlation between the presence of periodontal bacteria and clinical condition. The first case, a boy treated from age 2 to 6, showed periodontitis in the lower anterior region, which recovered to a good periodontal condition by a professional therapeutic approach. The second case is a girl, treated for 2 years from age 10, who presented with extremely enlarged gingiva and severe gingivitis, and a gingivectomy was carried out to eliminate the dental plaque accumulation. In both cases, periodontal bacteria were assessed periodically using PCR (Polymerase Chain Reaction) method, and the results compared with the clinical conditions. In both cases, increased numbers of periodontal bacteria were detected during the bad gingival condition period. In addition, Prevotella nigrescens and Prevotella intermedia were especially detected. Clinical condition seems to be influenced by the number of the periodontal bacteria present, which indicates that an effective monitoring of such bacteria would be beneficial for not only evaluating the current periodontal condition, but also for making an appropriate prognosis of a lesion.