The purpose of the present study was to quantify the effect of iron deficiency anaemia on the levels of HbA2, HbF, and HbA1C. Complete blood counts (CBC) were performed on 730 university students. Serum ferritin, HbA2, HbF, and HbA1C levels were determined for all microcytic/hypochromic subjects. It was found that 81 (11.1%) of the students were microcytic/hypochromic, of which 47 (58.1%) were found to be iron deficient. Twenty-six (32.1%) were b-thalassemia carriers, 4 (4.9%) were b-thalassemia carriers with iron deficiency and 4 (4.9%) remained undiagnosed. All the anaemic students were treated with oral iron and followed for 20 weeks. The mean HbA2 level rose significantly (from 1.89% ± 0.45 to 2.19% ± 0.53, P < 0.001) after iron treatment. HbF levels were not significantly different after iron treatment (0.94% ± 0.18 before and 0.95% ± 0.17 after treatment, P > 0.05). HbA1C fell significantly after iron treatment, from a mean of 6.15% ± 0.62 to 5.25% ± 0.45 (P < 0.001). In conclusion, iron deficiency must be corrected before making any diagnostic or therapeutic decisions based on HbA2 and HbA1C levels.