To provide basic information for β-thalassemia (β-thal) screening, genetic counseling and prenatal diagnosis (PND), we characterized β-thal mutations in Fujian Province, Southeastern China. A total of 16 different β-thal gene mutations were identified from 1058 patients. Of these, the IVS-II-654 (C>T) and codons 41/42 (-TCTT) were the most prevalent, accounting for 76.3% of the total mutations. Six gene mutations, IVS-I-1 (G>T), Cap +40 to +43 (-AAAC), codon 30 (A>G), +22 (G>A), codons 54-58 (-TTATGGGCAACCC) and the initiation codon (ATG>AGG) were characterized for the first time in the Fujian population. Furthermore, the following mutations, +22 (G >A), codon 36 (-C) and codon 30 (A>G), were identified for the first time in Chinese individuals. This was the first comprehensive mutation spectrum of β-thal mutations studied in Fujian Province, People's Republic of China (PRC).