This study investigated the microbial level of Streptococcus mutans and Lactobacillus spp. during an orthodontic treatment, and compare the data with untreated control subjects.Sixty young adult subjects were selected (average 20.5, DS 1.62), among which 40 underwent an orthodontic treatment (20 were treated with self-ligating brackets and 20 with conventional brackets) and 20 were controls. Plaque Index, salivary flow and buffering capacity of saliva were assessed before the beginning of the orthodontic treatment. Then the microbial counts were obtained by using an in-office bacteria test.The plaque index (PI) increased over time in each group as well as salivary flow, mostly in subjects treated with self-ligating brackets, suggesting a difference between conventional and self-ligating brackets. S.mutans showed a different trend of colonization in the two treated groups, as for subjects treated with conventional brackets it showed the greater value at the early stage of treatment (T1), followed by a decrease at T2. Lactobacillus spp. showed significant increase over time in the two treated groups, respect to the control group. Linear regression analysis showed no significant predictor for the microbial count at T2.The assortment of the various species of bacteria change over time during the orthodontic treatment, and seems to show different trends, depending on the type of orthodontic device. Consequently a periodical microbial monitoring using in-office bacteria tests, seems indicated.