The aim of our study was to assess the relationship between the concentration/activity of salivary stress biomarkers (cortisol, α-amylase) and the psychological profile of patients with oral lichen planus (OLP) and primary burning mouth syndrome (BMS). A total of 160 subjects participated in this cross-sectional study: 60 patients with OLP; 60 patients with primary BMS; 40 control subjects. Unstimulated whole saliva (UWS) was collected between 9 and 10 am. Salivary biomarkers were analyzed by enzyme-linked immunosorbent assay (ELISA). Psychological assessment was evaluated with the Depression, Anxiety, and Stress Scale (DASS-21). Patients with primary BMS had higher salivary cortisol concentrations and α-amylase activity (0.52 vs. 0.44 µg/dl; 160531 vs. 145804 U/L) compared with patients with OLP. Patients with primary BMS had statistically significantly higher scores for depression, anxiety, and stress compared with patients with OLP and control subjects (p <0.001, Kruskal-Wallis test). There was a strong positive correlation between anxiety and depression, stress and depression, stress and anxiety in patients with OLP and BMS (p <0.001 and p <0.001, respectively). There was a good positive correlation between symptom intensity (pain/burning) and psychological profile (depression, anxiety, stress) in patients with primary BMS (r=0.373, p=0.003; r=0.515, p <0.001; r=0.365, p= 0.004, respectively). Patients with BMS show a stronger association with mental disorders compared to patients with OLP. However, an interdisciplinary psychoneuroimmunological approach is equally important in both patient groups (OLP and BMS), regardless of whether mental disorders are the cause or the consequence.