Haemoglobinopathies may interfere with the haemoglobin A(Ic) (HbA(Ic)) measurement, leading to incorrect diagnosis and inappropriate treatment. It is essential that HbA(Ic) assays are capable of identifying haemoglobinopathies. We report two cases of haemoglobin New York (HbNY) discovered through HbA(Ic) analysis using capillary electrophoresis (Capillarys 2 Flex Piercing [C2FP], Sebia). We used these samples to evaluate the ability of three other HbA(Ic) assays to identify this variant: ion-exchange high-performance liquid chromatography (Variant II Turbo [VII-T],Bio-Rad); boronate affinity high-performance liquid chromatography (Ultra 2, Trinity Biotech) and immunoassay (Cobas c501 Tina-quant Generation 3, Roche Diagnostics). Each method was used for HbA(Ic) assay of in samples from two cases of heterozygous haemoglobinopathy: beta(0)-thalassemia/HbNY (Case 1) and HbA/NY (Case 2). Only the C2FP system detected HbNY (an additional peak appeared between HbA(Ic) and HbA(0)). Clinical laboratories should be aware of the limitations of their HbA(Ic) assay methods especially in geographic areas, where haemoglobinopathy prevalence is high.