Generalized chronic periodontitis (GCP) is a widespread disease. It has a serious negative impact on the quality of a patient’s life, posing a challenge to dentists all over the world. At present, standard therapy regimens for GCP adopted in the Russian Federation do not account for the mucosal barrier state, which is determined by a number of various factors, including the levels of secretory immunoglobulin A (sIgA). In our study, we attempted to assess the functional state of the mucosal barrier in patients with GCP and to provide a rationale for using immunotherapy aimed at restoring the effective barrier function of the oral mucosa. SIgA concentrations, which served as an indicator of the mucosal barrier state, were measured with ELISA. We found that patients with GCP had significantly lower sIgA concentrations in the oral fluid in comparison with healthy individuals. Although therapeutic procedures did help to increase sIgA levels, they still were much lower after therapy than in healthy volunteers (54.6 ± 30.5 µg/ml vs 151.2 ± 105.2 µg/ml). Increased permeability of the mucosal barrier caused sIgA to leak into the peripheral blood serum, where its concentration grew from 0.21 ± 0.28 µg/ml to 0.35 ± 0.47 µg/ml during the treatment course, suggesting damage to the mucosal integrity. This fact needs to be accounted for when treating patients with GCP.