Background: Recurrent aphthous stomatitis (RAS) is defined as a chronic inflammatory disease characterized by recurrent bouts of one or several shallow, rounded or ovoid, painful ulcers of oral mucosa that recur at intervals of a few days or up to 2–3 months and is of unknown etiology. The present study was conducted to assess salivary cortisol and dehydroepiandrosterone level in patients with recurrent aphthous stomatitis. Materials & Methods: 60 patients of recurrent aphthous stomatitis of both genderswere divided into 2 groups. Group I comprised of patients with recurrent aphthous stomatitis and group II comprised of healthy control. 2 mL of unstimulated whole saliva was collected and salivary cortisol and DHEA levels were measured using ELISA kit. Results: Group I had 25 males and 35 females and group II had 30 males and 30 females. 48 patients in group I and 22 in group II had salivary cortisol level >3 ng/ml and 12 in group I and 38 in group II had between 1.2–3 ng/mL. The difference was significant (P< 0.05).DHEA levels 48–61 pg/ml was seen in 30 patients in Group I and 7 in group II, <48 pg/ml was seen in 20 in group I and 48 in group II, >61 pg/ml was seen in 10 in group I and 4 in group II. The difference was significant (P< 0.05). Conclusion: Recurrent aphthous stomatitis patients exhibited higher mean salivary cortisol and dehydroepiandrosterone level compared to the healthy subjects.