To study the effect of donor TNF-alpha gene polymorphism on severe acute and extensive chronic graft versus host disease (GVHD), TNF-alpha gene polymorphism was analyzed by denaturing high performance liquid chromatography (DHPLC) and DNA sequencing in twenty-one patients with III/IV degree acute GVHD and twenty-seven patients with extensive chronic GVHD. The results showed that the frequency of TNF-alpha-308 (G/A) significantly increased in patients with III/IV degree acute GVHD compared to 0/I degree aGVHD patients (8/21 vs 1/28) (P < 0.01) and the frequency of TNF-alpha-308 (G/A) is significantly higher in patients with extensive chronic GVHD than in patients without chronic GVHD (7/23 vs 1/17) (P < 0.05). However, the frequency of TNF-alpha-238 (G/A) does not significantly changed in patients with III/IV degree acute GVHD and extensive chronic GVHD. In conclusion, the TNF-alpha-308 (G/A) is likely to contribute to high risk for III/IV degree acute GVHD and extensive chronic GVHD.