Although the main cause of gastrointestinal stromal tumor (GIST) is gain‐of‐function mutations in thec‐kitgene in the interstitial cells of Cajal, concomitant genetic or epigenetic changes other thanc‐kitappear to occur in the development of metastasis. We sought to identify the genes involved in the metastatic process of gastric GIST. Microarray analysis was performed to compare gene expressions between three gastric GIST and four metastatic liver GIST. Expression levels were higher for 165 genes and lower for 146 genes in metastatic liver GIST. The upregulation of five oncogenes and downregulation of four tumor suppressor genes including versican and CD9 were confirmed by quantitative reverse transcriptional PCR. Immunohistochemistry in 117 GIST revealed that protein levels of versican and CD9 were higher and lower, respectively, in metastatic GIST. High expression of versican and low expression of CD9 in 104 primary gastric GIST correlated with poor disease‐free survival (P = 0.0078 andP = 0.0018). In addition to thec‐kitgene mutation, genetic or epigenetic changes other thanc‐kitplay important roles in the metastatic process. In particular, versican and CD9 are potential prognostic markers in gastric GIST. (Cancer Sci2011; 102: 883–889)