OBJECTIVE: To identify clinical, salivary, and bacterial changes during orthodontic treatment with follow-up to 24 months. METHODS: In 30 patients, clinical (decayed, missing, and filled surfaces [DMFS], O'Leary's plaque index, and plaque pH), salivary (unstimulated and stimulated saliva, buffer capacity, pH, and occult blood), and bacterial (Streptococcus mutans and Lactobacillus) markers were evaluated. A questionnaire was employed to evaluate their hygienic-dietary habits. Data were analyzed by ANOVA, logistic regression and Spearman's correlation. RESULTS: DMFS increased significantly, whereas the plaque index diminished, plaque pH was more acidic (p = 0.23), and unstimulated salivary flow showed significant differences during the treatment (p = 0.013). Stimulated saliva flow increased in females after the placement of appliances; buffer capacity was diminished in males during the therapy; salivary pH remained at basal values. Bacterial levels and occult blood increased to high-risk levels and were not statistically significant different between genders (p > 0.05). Two major relationships were confirmed: initial plaque with use of dental aids (r = 0.429; p = 0.018) and final DMFS with unstimulated salivary flow (r = -0.372; p = 0.043). CONCLUSIONS: The increase in retentive surfaces increased the bacterial levels, plaque pH became acidified, and gingival damage was greater. Buffer capacity was altered but maintained a healthy salivary pH during the treatment.