Objectives -Thalassaemia is widely found in Southwestern China. Characterisation of -thalassaemia can improve screening and prenatal diagnosis for at-risk populations. Design A retrospective study. Methods In this study, the levels of haemoglobin alpha 2 (HbA(2)) and haemoglobin alpha (HbA) were analysed by gender for a total of 15067 subjects screened by capillary electrophoresis. The cut-off value with the highest accuracy was established to identify -thalassaemia in 723 patients suspected to have this disease. Haematological and electrophoretic characterisation of eight common types of -thalassaemia were analysed in 486 -thalassaemia subjects. Results HbA levels were significantly higher in men than in women, but there was no significant difference on HbA(2) levels. A new cut-off value for the diagnosis of -thalassaemia (HbA(2)4.0%) with the highest accuracy was proposed for the studied populations. Haemoglobin (Hb) was significantly higher in men compared with women (p<0.05), whereas no statistically significant differences were found for mean cell volume (MCV), mean cell haemoglobin (MCH), HbA and HbA(2). The haemoglobin E (HbE) group showed comparatively higher values for haematological indices (Hb, MCV and MCH) than the other genotypes in heterozygous -thalassaemia groups (p<0.05), and -28 (A>G) (HBB (-globin):c.-78A>C) had significantly higher HbA(2) values compared with other -thalassaemia. Conclusions Ethnic groups have diversified -globin gene mutations and considerable haematological variations. Our study will lay the foundation for screening programmes and clinical management of thalassaemia in Southwestern China.