The aim of this study was to evaluate changes of microbiota in ten patients undergoing orthodontic treatment. For each patient clinical examination of gingival index (GI) and plaque index (PI) were performed at the first molars at: baseline (T1), 2 (T2), 4 (T3) and 12 weeks (T4). At the same time subgingival plaque and tongue samples were taken for the microbiological study. Clinical results showed that at T4, the mean PI score was significantly lower than T1 and the GI was markedly reduced. Microbiological results showed that at T1 and T4 facultative aerobic bacteria were prevalent, whereas anaerobic bacteria were more common at T2 and T3.