Plain Language Summary Little is known about the relationship between iron deficiency and autoimmune disease. By using a national-level database in Taiwan, we noted a meaningful association between iron deficiency anemia (IDA) and later autoimmune disease development. Our study extends the known disease range and recommends that physicians be alert for the occurrence of autoimmune disease after an IDA diagnosis. The subgroup analysis indicated that, among patients with IDA, female patients and patients with the simultaneous chronic diseases of allergic rhinitis, urticaria, cancer, chronic obstructive pulmonary disease (COPD), hyperlipidemia, or hypertension had a significantly higher risk of autoimmune disease. The risk of autoimmune disease was considerably higher within the 2 years after an IDA diagnosis.