The aim of this work was to investigate the association between recurrent aphthous stomatitis (RAS) and salivary thiocyanate levels. The sample comprised men and women of age ranging from 15 to 55 years, who were allocated to four groups: 28 patients in RAS active phase (group 1); 28 patients in RAS remission phase (group 2); 29 smokers (group 3); 26 non-smokers without RAS (group 4). Samples of whole saliva mechanically stimulated were collected, and thiocyanate levels were measured. The results were analyzed by ANOVA and paired t-test. Mean salivary thiocyanate values were 0.55 mM, 0.64 mM, 2.36 mM and 0.96 mM in groups 1 (active RAS), 2 (remission RAS), 3 (smokers) and 4 (control), respectively. There was no significant difference in thiocyanate levels when groups 1 and 2 were compared with group 4. Group 3 showed a significantly higher thiocyanate concentration when compared with groups 1, 2 and 4 (P < 0.05). There was no significant difference in thiocyanate levels between groups 1 and 2 (P > 0.05). It is therefore suggested that there is no association between RAS and salivary thiocyanate levels.