The objective of this project was to characterize the salivary proteome of patients with recurrent aphthous stomatitis using mass spectrometry-based proteomics(nLC-MS/MS) and assess its clinical usefulness in identifying the most representative biological and molecular processes during the course of lesions. To do this, we conducted a case-control study, analyzing the saliva of healthy controls and patients with recurrent aphthous stomatitis during a complete ulcerative cycle (active ulcers and absence of lesions).