Previous studies have shown during the orthodontic treatment, the prevalence of active caries lesions (ACL) in 30 to 70% of patients. To evaluate the effect of orthodontic treatment on salivary properties considering caries development. Twenty two individuals (11-22 years) were assessed regarding caries, oral hygiene, sugar exposure, salivary flow rate (SFR), buffering capacity, pH, carbonic anhydrase VI (CA VI) and amylase activity, at baseline, 1, 3 and 6 months after the orthodontic appliances placement. Caries index was determined by Nyvad criteria. CA VI and amylase activities were performed by zymography and ELISA, respectively. Buffering capacity decreased after 3 months (P < 0.0001) and showed positive correlation with pH at baseline and after 1 month in individuals who did not develop active caries lesions. Amylase activity decreased after 1 and 6 months (P = 0.0003) and presented positive correlation with CA VI in patients who developed ACL. SFR increased after 1 month (P = 0.0283) and showed positive correlation with CA VI activity after 3 months in individuals who did not develop ACL. Salivary pH showed negative correlation with CA VI after 1 month in patients who did not develop ACL. ACL were firstly diagnosed after 3 months. The present study demonstrated that saliva of individuals under orthodontic treatment is subjected to changes in properties that have implications on the onset of ACL.