Objective To investigate the carrier ratio and the genotype of thalassemia among students of secondary school in Chongzuo, Guangxi. Methods From June 10-20,2008 among 7 regions of Chongzuo, 1 secondary school was randomly chosen from each region, and the number of student volunteers was determined by 0.5‰ proportion of the local population size. 1097 students were screened, including 515 boys and 582 girls of 12-16 year olds. Among them, 968 cases were Zhuang (438 boys and 530 girls) 128 cases were Han (76 boys and 52 girls) and one case was Yao nationalities (boy). Analysis of blood cells was detected by Cell Dyn 1700 automatic hemocyte analysator while hemoglobin F (HbF) and hemoglobin A2 (HbA2) were detected by hemoglobin autoanalyse variant. Among those with HbA2≥ 4% that belonged to β-thalassemia before α and β-thalassemia gene were analyzed to identify the genotypes. IfHbA2 was <4% but MCV≤80 fl, α-thalassemia gene was analyzed. Results Among 1097 cases,218 wereα-thalassemia (19.87%), 50 were β-thalassemia (4.56%) and 13 were combination of α β-thalassemia (1.19%). The overall detected ratio was 25.62%. 133 cases with thalassemia were boys (25.83%) and 148 were girls (25.43%) with no significant difference(P>0.05). 255 cases of thalassemia were Zhuang (26.34%), and 25 were Han nationality (19.52%). The detected ratio among Zhuang nationality was higher than in Hun nationality and with significant difference statistically (P<0.01). 3 kinds of deletion (-α3.7/,-α<4.2>/, --SEA/) and another 3 kinds of non-deletion (αα CS/, αα WS/, αα QS/) α-thalassemia genotype were identified, with a higher rate of ααWS/. Among the β-thalassemia genotype, CD41-42 appeared the most common genotype. MCV of thalassemia was lower than in the controls, with significant difference (P<0.01). 78-90 fl of α-thalassemia was detected from the MCV specimen. If taken MCV<79 fl as the positive phenotype of thalassemia, 32 cases were misdiagnosed. The rate of missed diagnosed cases was 2.97%. Conclusion Rate of thalassemia carder among students of secondary school in Chongzuo, Guangxi was considered to be high, especially those belonged to Zhuang nationality were higher than the Hans. The carrier rate of ααWS/was higher, with CD41-42 the most common genotype.