OBJECTIVES: Studies suggest that iron deficiency anaemia (IDA) is associated with higher HbA1c levels. We conducted a control­case study to investigate the effect of IDA on HbA1c levels, measured by two commonly used methods, in non-diabetic individuals. DESIGN AND METHODS: A total of 122 patients were included, 61 patients with IDA and 61 patients without anaemia. HbA1c was measured by both ion exchange HPLC Variant II Turbo BioRad and immunoturbidimetry (IT) Tina Quant II Roche Diagnostics in each sample. HbA1c results were compared between groups. For correlation analysis, patients were considered altogether. RESULTS: There was a significant difference between the results of HbA1c in patients with IDA [HPLC 5.6 ± 0.4% (38 ± 4.4 mmol/mol) and IT 5.7 ± 0.4% (39 ± 4.4 mmol/mol)] and those measured in patients without anaemia [HPLC 5.3 ± 0.4% (34 ± 4.4 mmol/mol) and IT 5.3 ± 0.3% (34 ± 3.3 mmol/mol)], (p < 0.001). Significant negative correlations were observed between total haemoglobin (Hb), haematocrit, mean corpuscular volume (MCV) and ferritin with HbA1c values measured by IT (r = − 0.557; r = − 0.539; r = − 0.488; r = − 0.499; p < 0.01; respectively). These negative correlations were weaker with HbA1c measured by HPLC (r = − 0.272; r = − 0.250; r = − 0.273; r = − 0.229 for Hb, haematocrit, MCV and ferritin; p < 0.05; respectively). HbA1c results were higher in patients with moderate and severe anaemia. However mild anaemia did not show significant effects on HbA1c results measured by both methods. CONCLUSIONS: IDA affects HbA1c results and this effect is dependent on anaemia degree. These upward changes are statistically significant but they may be not clinically relevant when the overall variability of the HbA1c test is considered. The presence of slight anaemia is likely to have a minor effect on HbA1c levels favouring its use to diagnose diabetes in patients with mild anaemia.