Objectives: The aim of this study was to identify changes in the oral environment with clinical, salivary and bacterial risk markers after placement of fixed orthodontic appliances on permanent dentition. Material and Methods: With ethical approval, we used different techniques to analyzed clinical, salivary and bacterial risk markers in 34 patients (mean age, 16.7 ± 5.2 years), 14 males and 20 females; before starting orthodontic treatment and 1 month after. Clinical risk markers (decayed, missing, and filled surfaces [DMFS], O'Leary´s plaque index, and plaque pH); salivary markers (unstimulated and stimulated saliva flow rate, buffer capacity, pH, and occult blood in saliva) and bacterial counts (Streptococcus mutans and Lactobacillus). Data were analyzed by paired t-test and χ 2 test. Results: This study showed that orthodontic appliances increased the stimulated salivary flow rate (p=0.0001), buffer capacity (p=0.0359), salivary pH (p=0.0246) and occult blood in saliva (p=0.0305). Bacterial levels increased slightly after 1 month of treatment, without statistical significance. Between genders, initially we observed differences in: stimulated saliva (p=0.0019), buffer capacity (p=0.0381) and plaque pH (p=0.0430); after treatment the unstimulated saliva (p=0.0026) showed differences. Conclusions: Orthodontic treatment changes the oral environmental factors, promotes an increase in stimulated flow rate, buffer capacity and salivary pH, which augment the anti caries activity of saliva. In contrast, increased occult blood indicated more gingival inflammation, apparently because augmented the retentive plaque surfaces and the difficult to maintain a good oral hygiene, rinsed the bleeding in saliva by periodontal damage.