This study aimed to examine the role of stress in the occurrence of recurrent aphthous stomatitis (RAS) and oral lichen planus (OLP), as well as to analyze the efficacy of saliva, urine, and serum cortisol levels as markers of stress. This study included 30 subjects with RAS (Group A), 30 with OLP (Group B), and 30 controls (Group C). The serum, salivary, and urinary cortisol levels were measured using electro-chemiluminescence immunoassay. The results were analyzed using the independent t-test, and a statistically significant difference (P = 0.000) was observed between the study and control groups. Further analysis was done using ANOVA and post-hoc tests. The results of this study suggest that RAS and OLP patients had higher cortisol levels than controls, indicating that stress acts as a co-factor in the pathogenesis of RAS and OLP. Although urinary cortisol level was found to be the best indicator of stress, saliva can also be used as a reliable marker. (J Oral Sci 58, 237-240, 2016)