The aim of this study was to analyse serum IgG levels and salivary secretory IgA (sIgA) levels in human dentine extract (HDE) before (T0) and 6 months after (T6) orthodontic treatment and to correlate anti-HDE autoantibodies to root resorption. Fifty orthodontic patients were selected, 19 males (15.6 ± 8.5 years) and 31 females (21.4 ± 11.2 years), 19 in the mixed dentition (10.3 ± 1.9 years) and 31 in the permanent dentition (24.6 ± 9.9 years). Fifty individuals not undergoing orthodontic treatment matched by gender and age were selected as the controls. Periapical radiographs of the upper central incisors and saliva sampling were obtained of all patients at T0 and T6. Serum samples were collected from the permanent dentition patients (n = 31). Antibody levels were determined by means of immunoenzyme assay. At T6, root resorption was classified as grade 0 (no resorption), grade 1 (slight resorption), and grade 2 (moderate to severe resorption). Differences between antibody levels at T0 and T6 and among different grades of resorption were determined by paired t- and Kruskal-Wallis tests, respectively. Spearman's rank correlation coefficient was applied to detect correlation between sIgA and IgG levels, and logistic regression to determine the association of root resorption grade and the studied variables. Differences were considered significant at P < 0.05. Serum anti-HDE IgG levels decreased (P < 0.01) in grade 2 root resorption patients during treatment and was not correlated to salivary sIgA levels or other variables. Patients who had grade 2 root resorption at T6 showed higher levels of anti-HDE sIgA (P < 0.001). Anti-HDE sIgA levels at T0 and root shape were the main factors associated with the degree of root resorption. The results suggest that variations to systemic and local humoural immune response to dentine antigens may occur during orthodontic treatment. High levels of salivary sIgA before treatment were associated with more advanced lesions after 6 months of treatment.