The present study evaluated microbiological and clinical changes occurring during the first six months of orthodontic therapy with fixed and removable appliances and the consequent risk for gingivitis and periodontal disease. This study was justified by the disagreement among different authors: only some of them reported gingivitis development and changes in dental plaque composition during orthodontic therapy with fixed appliances, others did not. Thirty, 7-to-15-year-old children, fifteen with fixed and fifteen with removable appliances, previously motivated to oral hygiene, completed the study. They were clinically examined by a dentist at baseline and at the end of the study. Three supra and subgingival microflora samples were collected from the first molars, when the appliances were inserted (T0), 6-8 weeks later (T1) and 6-7 months later (T2). Microflora was examined using dark-field and light microscopes and cultural methods. An indicator of healthy status (percentage of Gram positive cocci in total bacterial count) and some risk indicators for gingivitis (bacterial count evaluated with light microscope, percentage of Gram negative rods) and for periodontitis (motile rod and spirochete percentages, presumptive Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis prevalence) were investigated. Patients with fixed appliances were clinically healthy at T2; yet they showed significantly increased counts, motile rods, subgingival spirochetes and a decrease of Gram positive cocci. At T2, patients with removable appliances were clinically healthy and the only significant microbiological changes were supragingival motile rods and subgingival spirochetes. These data suggest that in the oral hygiene motivated patients of the present study, gingivitis and periodontitis do not occur, during the first six months of treatment: the significant modification of oral microbiota, shown by subjects with fixed appliances, however, suggests that the risk for gingivitis in the following months of therapy is still high and the risk for periodontitis cannot be excluded.