Problem Considered- Recurrent Aphthous Stomatitis (RAS) is one of the most common and poorly understood mucosal disorders. Psychological anxiety is considered one of the causative factors which alters cortisol levels in the body. Nitric Oxide (NO) is a cytotoxic molecule and is produced from neural tissue, blood vessels, macrophages and T-lymphocytes. The aim of the present study was to estimate and compare the levels of salivary cortisol and NO in patients with RAS in active phase and remission phase and in normal healthy individuals. Also to correlate the salivary cortisol and NO levels with anxiety levels of the patients. Methods- the present prospective study comprised of 25 RAS patients and 25 sex and age matched normal healthy individuals. Saliva samples were collected from RAS patients once in active ulcer phase and once in remission phase. A questionnaire called ‘State-Trait anxiety test’ was filled by the patients. One part of collected saliva was analysed for NO by Griess reagent and spectrophotometer and the other part for cortisol by ELISA method. Results- the study showed that both salivary cortisol and NO were significantly more in RAS patients when compared to the control group. Within the study group there was a significant difference in both the salivary cortisol levels and NO levels between the stage of active ulcer and stage of remission. The anxiety levels were more in RAS patients than the control group but this was not statistically significant. Poor correlation was seen among the levels of anxiety, salivary cortisol and salivary NO. Conclusion- salivary cortisol and NO can be used as a diagnostic feature and possible treatment of RAS.