Background Recurrent aphthous ulceration (RAU) is one of the most common oral mucosal diseases, some of which may be secondary to haematologic deficiencies. This meta-analysis aims to evaluate the association between haematologic deficiencies and RAU. Material and methods Case control studies were identified using a predefined search strategy that compared the difference in haematologic deficiencies between a RAU group and a control group. A meta-analysis was performed to estimate the combined odds ratios (ORs) and 95% confidence intervals (95% CIs) in a fixed-effects model and a random-effects model, as appropriate. Results In this meta-analysis, nine case control studies, including total 710 cases in RAU groups and 602 cases in control groups, were considered eligible for inclusion. Overall, the combined results based on all studies showed that the rate of haematinic deficiencies was significantly high in the RAU group (vitamin B12: OR = 3.75, 95% CI: 2.38-5.94; folic acid: OR = 7.55, 95% CI: 3.91-14.60; ferritin: OR = 2.62, 95% CI: 1.69-4.06; and haemoglobin: OR = 1.77, 95% CI: 1.12-2.80). Conclusion This meta-analysis suggests that haematologic deficiencies could be a significant risk factor for RAU. Thus, screening and treating any haematologic deficiencies may play an important role in preventing the occurrence of RAU.