Objective: To investigate the methylation status of CpG island in E-cadherin(CDH1), P16INK4a(P16)promoter region ,and to analyze their role in gastrointestinal stromal tumor (GISTs). Methods: A total of 56 surgically resected GISTs were obtained from January 2003 to December 2005. The routine H&E-stained sections and CD117, CD34-immunoreactions were reviewed to verify the morphologic diagnosis. Methylation status of the CDH1, P16INK4a promoter region was analyzed by methylation specific polymerase chain reaction (MSP) from chemically modified DNA after Na-bisulfite treatment. Results: The frequency of CDH1gene methylation was 32% (18 of 56) in GISTs. The rate was 9% (1 of 11), 21% (4 of 19), 41.6% (5 of 12), and 57% (8 of 14) for very low risk, low risk, intermediate risk, and high risk GISTs; P16INK4a methylation was found in 19 of 56(34%) cases. The rate was 0% (0 of 11), 16% (3 of 19), 50% (6 of 12), and 71% (10 of 14) for very low risk, low risk, intermediate risk, and high risk GISTs. Statistical analysis indicated that of the 56 cases, there was significant association of CDH1 and/or P16INK4a methylation status with tumor malignant behavior (methylation rate 23/56, 41%, P＜0.01) and site (P＜0.05). Conclusion: E-cadherin (CDH1) and/or P16INK4a promoter hypermethylation is strongly associated with risk grade, may be a useful biomarker for GISTs risk assessment, and may shed light on new therapeutic options to treat GISTs