AIMS Haemophilia B (HB) is an X-linked recessive haemorrhagic disorder caused by F9 mutations. In this study, we performed molecular analysis of 107 Chinese HB patients and analysed the F9 mutation spectrum of Chinese HB patients. METHODS 107 Chinese HB patients were enrolled in this study. Direct sequencing of the whole F9 or mutation scanning of exon 1 to exon 7 by high resolution melting (HRM) curve analysis combined with direct sequencing of exon 8 was used to identify the mutations in these patients. RESULTS 78 different F9 mutations were identified in the 107 HB patients. The mutations were composed of 50 missense mutations, 14 nonsense mutations, nine small deletions, three splice site mutations and two small insertions. Forty-three of 78 mutations were located in factor IX (FIX) catalytic domain. Among the 78 mutations, 20 have not been previously reported. CONCLUSIONS The F9 mutations were heterogenous and the missense mutations were the most prevalent gene defects in Chinese HB patients.