Stress causes an increase in cortisol and amylase. Recurrent aphthous stomatitis (RAS) results due to a multitude of causes, amongst which stress is one of the most important. Aim of the study was to estimate the level of stress, serum cortisol, salivary cortisol, amylase and electrolytes in subjects with RAS. 34 subjects with RAS (cases) were compared with 34 controls. Stress was measured using state trait anxiety inventory (STAI). Serum cortisol (Radioimmunoassay), Salivary cortisol, amylase (ELISA) and electrolytes (Flame photometry) were measured. Statistical analysis was done using SPSS 18.0 version software. The mean STAI scores were 48.71 ± 4.6 in cases and 46.74 ± 6.4 in controls (P = 0.13). The mean salivary cortisol concentration was 3.35 ± 1.8 ng/dl in cases and 3.65 ± 2.5 ng/dl in controls (P = 0.78). The mean salivary amylase was 155.09 ± 116.1 U/ml in cases and 128.74 ± 86.3 U/ml in controls (P = 0.49). The salivary sodium (0.24 ± 0.4 in both groups) and potassium (0.65 ± 0.5 in cases and 0.82 ± 0.4 in controls; P = 0.07) was not different in the two groups (electrolytes in mEq/dl). No correlation was seen between the salivary stress markers and STAI scores. Though stress was higher in RAS group none of the measured parameters were different from the control group. Stress may cause RAS but, in this study, there was no change in the salivary homeostasis.