Background: Recurrent aphthous stomatitis (RAS) is one of the most common oral mucosal disorders with a prevalence of 50-66%. The prevalence of hematinic deficiencies including ferritin and vitamin B12 deficiencies and their role in the prophylaxis and development of RAS is not well known. Many studies have demonstrated a high prevalence of hematinic deficiencies in patients with RAS. This study aimed to compare the serum level of ferritin and vitamin B12 in patients with recurrent aphthous ulcers and healthy controls. Subjects, Materials and Methods: The data were collected from patients who needed blood analysis to exclude anemia from November 2020 to May 2021. The study was approved by the institutional ethics committee. After recording patients' demographics ( age, gender, occupation, address)  5ml of blood was drawn from patients and controls in educational laboratories centrifuged at 3000 rpm for 10 minutes, then serum was stored at -20°C till the time of assessment of both serum ferritin and vitamin B12. The data were expressed as Mean ± SD. Students Unpaired t-test was used for comparing biochemical parameters between patients and controls and a p-value of <0.05 was considered as a statistically significant while a p-value of<0.001 was considered highly statistically significant. Results: A total of 30 RAS patients and 30 healthy control with age and gender matches were included. In the present study statistically, significant differences were observed in the serum level of ferritin and vitamin B12 between the two groups, 40% of the patients had low serum ferritin levels and 56.6 % of the patients had low serum vitamin B12 levels. Conclusion: Measuring serum ferritin and vitamin B12 levels are necessary for patients with recurrent aphthous stomatitis. It is also important for recurrent aphthous ulcer patients to have a nutritional diet containing iron and vitamin B12 to prevent the recurrence of aphthous ulceration