Background/purpose: The aim of this study was to identify salivary changes during orthodontic treatment with follow-up for 30 months. Materials and methods: In 25 patients salivary markers (unstimulated and stimulated saliva, buffer capacity, and pH) were evaluated. The decayed, missing, and filled surfaces (DMFS) index, plaque index (O’Leary), and a questionnaire were employed to evaluate patient’s hygiene and dietary habits. Data were analyzed by a paired t test, a MANOVA model with repeated-measures analysis, a multiple-regression analysis, and a Spearman correlation test. Results: During treatment, the DMFS index increased significantly (P=0.007), the plaque index decreased by 28.4%, and the unstimulated salivary flow showed differences (P=0.009). Stimulated saliva flow increased in females after placement of the appliance; the buffer capacity diminished in males during therapy, and salivary pH remained at basal values. Statistically significant associations were revealed by the multiple-regression analysis and Spearman test; the salivary factors of the unstimulated salivary flow rate, buffer capacity, and pH were associated with the final DMFS index (P<0.0001); the frequency of eating food between meals was associated with the DMFS index (r=0.4918; P=0.0125), and the frequency of changing the toothbrush was associated with the DMFS index (r=−0.4299; P=0.0320). Conclusion: The multiple caries-related factors examined in this study changed during orthodontic treatment, but many of these stayed within normal values. Saliva is an important protector of oral mucosal tissues and teeth, and its constant role is supported even in adverse conditions, such as the presence of orthodontic appliances in the mouth.