BACKGROUND The clinical syndrome of thalassemia intermedia (TI) results from the beta-globin genotypes in combination with factors to produce fetal haemoglobin (HbF) and/or co-inheritance of alpha-thalassemia. However, very little is currently known of the molecular basis of Chinese TI patients. METHODS We systematically analyzed and characterized beta-globin genotypes, alpha-thalassemia determinants, and known primary genetic modifiers linked to the production of HbF and the aggravation of alpha/beta imbalance in 117 Chinese TI patients. Genotype-phenotype correlations were analyzed based on retrospective clinical observations. RESULTS A total of 117 TI patients were divided into two major groups, namely heterozygous beta-thalassemia (n = 20) in which 14 were characterized as having a mild TI with the Hb levels of 68-95 g/L except for five co-inherited alphaalphaalphaanti-3.7 triplication and one carried a dominant mutation; and beta-thalassemia homozygotes or compound heterozygotes for beta-thalassemia and other beta-globin defects in which the beta+-thalassemia mutation was the most common (49/97), hemoglobin E (HbE) variants was second (27/97), and deletional hereditary persistence of fetal hemoglobin (HPFH) or deltabeta-thalassemia was third (11/97). Two novel mutations, Term CD+32(A-->C) and Cap+39(C-->T), have been detected. CONCLUSIONS Chinese TI patients showed considerable heterogeneity, both phenotypically and genotypically. The clinical outcomes of our TI patients were mostly explained by the genotypes linked to the beta- and alpha-globin gene cluster. However, for a group of 14 patients (13 beta0/betaN and 1 beta+/betaN) with known heterozygous mutations of beta-thalassemia and three with homozygous beta-thalassemia (beta0/beta0), the existence of other causative genetic determinants is remaining to be molecularly defined.