Serum anti-gastric parietal cell (GPCA), anti-thyroglobulin (TGA), and anti-thyroid microsomal antibodies (TMA) can be found in some recurrent aphthous stomatitis (RAS) patients. This study mainly assessed whether serum GPCA, TGA, TMA and RAS itself played significant roles in causing anemia and hematinic deficiencies in TGA/TMA-positive RAS patients with GPCA positivity (GPCA+/TGA/TMA/RAS patients) or negativity (GPCA−/TGA/TMA/RAS patients). Methods: The mean corpuscular volume (MCV) and mean blood hemoglobin (Hb), iron, vitamin B12, and folic acid levels were measured and compared between any two of the four groups of 15 GPCA+/TGA/TMA/RAS patients, 69 GPCA−/TGA/TMA/RAS patients, 240 all autoantibodies-negative RAS patients (Abs−/RAS patients), and 342 healthy control subjects. Results: GPCA+/TGA/TMA/RAS patients had significantly lower mean Hb (for men only) and vitamin B12 levels as well as significantly greater frequencies of Hb, iron, and vitamin B12 deficiencies than healthy control subjects. GPCA+/TGA/TMA/RAS patients had lower serum vitamin B12 level and higher MCV as well as a significantly greater frequency of vitamin B12 deficiency than GPCA−/TGA/TMA/RAS patients. Furthermore, both GPCA−/TGA/TMA/RAS and Abs−/RAS patients did have significantly lower mean Hb, MCV, and iron levels as well as significantly greater frequencies of Hb, iron and vitamin B12 deficiencies than healthy control subjects. There were no significant differences in blood data between GPCA−/TGA/TMA/RAS and Abs−/RAS patients Conclusion: Both serum GPCA positivity and RAS itself are the contributing factors causing anemia and hematinic deficiencies in GPCA+/TGA/TMA/RAS patients. RAS itself but not TGA/TMA positivity plays a significant role in causing anemia and hematinic deficiencies in GPCA−/TGA/TMA/RAS patients.