OBJECTIVE: To investigate the types and frequency of gene mutations in children with thalassemia in Kunming, Yunan Province. METHODS: A biochemical screening for thalassemia was performed by testing RBC fragility, MCV and hemoglobin electrophoresis on 1338 children from Kunming, Yunnan Province. Genetic diagnosis was performed on the children with α-thalassemia by gap-PCR and on the children with β-thalassemia by PCR-RDB. RESULTS: The positive rate of the biochemical screening for thalassemia was 11.36% (152 cases). The positive rate of genetic diagnosis was 8.59% (115 cases). Of the 115 cases, α-thalassemia was found in 43 cases, β-thalassemia in 68 cases and α-combined-β thalassemia in 4 cases.--SEA/αα accounted for 47%, -α4.2/αα accounted for 21%, and HbH disease accounted for 14%. Six genotypes were found in 68 cases of β-thalassemia and the mutation frequency of βE was the highest (32%), followed by CD41-42 (24%), CD17 (23%), IVS-II654 (10%), CD71-72 (10%), and -28 (1%). CONCLUSIONS: The frequency of gene mutations for thalassemia is high in children from Kunming, Yunnan Province. Premarital and prenatal screenings and genetic diagnosis for thalassemia should be carried out in this area.