Recurrent aphthous stomatitis (RAS) is one of the most common oral mucosal disorders. The aim of the study was to determine any association between anxiety levels and concentrations of salivary and serum cortisol in patients with RAS. It has been suggested that stress with its presumed effects on the immune system, constitutes one of the major causative agents of RAS. The concentrations of salivary and serum cortisol were measured in 38 patients with recurrent aphthous stomatitis, and 38 healthy controls. Salivary and serum cortisol levels were measured using a Luminenscent Immunoassay (LIA) method. Anxiety levels were evaluated using Spielberger's State-Trait Anxiety Inventory which measures both trait anxiety as a general aspect of personality (STAI-T) and state anxiety as a response to a specific situation (STAI-S). The salivary cortisol levels were 1.44 (± 0.58) μg dl^-1 in RAS patients and 0.91 (± 0.56) μg dl^-1 in controls (p = 0.001), while the serum cortisol levels were 3.13 (± 1.59) μg dl^-1 in RAS patients and 1.89 (± 1.11) μg dl^-1 in controls (p = 0.001). The state anxiety levels (STAI-S) were 48.85 (± 9.7) in RAS group and 39.45 (± 7.5) in control group (p = 0.001). The trait anxiety levels (STAI-T) were 49.78 (± 13.02) in RAS group and 38.49 (± 10.31) in control group (p = 0.001). Salivary and serum cortisol concentrations and state and trait anxiety levels in RAS were significantly higher than those in the control group. Our results suggest that stress may be involved in the pathogenesis of RAS.