The objective of this work was a correct statistical comparison of two assay methods for determination of glycated haemoglobin HbA1c. The immunoturbidimetric determination of HbA1c was performed in two ways: using an automatic analyser Hitachi 912, calibrated according to the IFCC reference system (International Federation of Clinical Chemistry and Laboratory Medicine) and using an analyser Advia 1200 and the NGSP reference system (National Glycohaemoglobin Standardization Program). For statistical comparison of these two analytical methods several advanced regression methods were used, which respect random errors of both compared methods. Specifically, Deming regression with and without weights, orthogonal regression, and Passing-Bablok regression were employed. The results demonstrate that the investigated analytical assay methods do not correspond to each other. The summarized results indicate usefulness of better harmonisation of two existing reference systems.