Recurrent aphthous stomatitis is a common oral mucosa disease, with no specific etiology. Atopy has been implicated in the development of this disease. In this study, the salivary levels of immunoglobulin E (IgE) and eosinophil cationic protein (ECP) were measured as allergy-related biomarkers in patients with aphthous stomatitis. In this case-control study, non-stimulated saliva was collected from 85 participants and IgE and ECP were measured. Data were analyzed in SPSS 20 through the Mann-Whitney test, and p<0.05 was considered significant. The salivary levels of IgE and ECP were 1.11±0.65 Iu/ml and 26.93±6.95 ng/ml in the case group and 0.73±0/39 Iu/ml and 21.97±6.72 ng/ml in the control group. There was a significant difference between the two groups in terms of salivary levels of IgE and ECP (p=0.001). The results showed that patients with oral aphthous had higher levels of salivary IgE and ECP than controls. Therefore, measurement of these biomarkers may be useful in the initial evaluation of patients with aphthous stomatitis.