The causes of iron deficiency vary significantly during different stages of life, and according to gender and socioeconomic circumstances. Although dietary iron is important, iron deficiency anemia (IDA) is mostly attributed to blood loss and may be the presenting clinical feature of occult bleeding from the gastrointestinal (GI) tract heralding underlying malignancy. Conventional GI diagnostic workup fails to establish the cause of iron deficiency in about one third of patients. However, abnormal iron absorption caused by hereditary iron-refractory iron deficiency anemia (IRIDA) or acquired disease is increasingly recognized as an important cause of unexplained iron deficiency. The recent availability of convenient, non-invasive screening methods to identify celiac disease, autoimmune atrophic gastritis and Helicobacter pylori infection has greatly facilitated the recognition of patients with these entities. Cure of previously refractory IDA by H pylori eradication provides strong evidence supporting a cause-and-effect relation. The intriguing recent observations of H pylori antibodies directed against epitopes on gastric mucosal cells in atrophic gastritis imply an autoimmune mechanism triggered by H pylori and directed against gastric parietal cells by means of antigenic mimicry. Improved understanding of the role of abnormal iron absorption in IDA has important implications for current concepts related to the pathogenesis and management of IDA.