BACKGROUND: We intended to find predictive markers in advanced gastrointestinal stromal tumor patients treated with sunitinib. METHODS: Korean patients who received sunitinib after imatinib failure for advanced gastrointestinal stromal tumor were studied. Genotyping for KIT and PDGFRA were performed. Immunohistochemical stain for PDGFR-α, PDGFR-β, and vascular endothelial growth factor (VEGF) was performed. RESULTS: A total of 22 patients were analyzed. Their median age was 55.1 years, and the male to female ratio was 12:10. Response rate of sunitinib was 30.4% and median progression-free survival (PFS) was 10.1 months. In sunitinib treatment, VEGF expression was related to a favorable response (P=0.002) and long PFS (P=0.020) in univariate analysis. CD34 (P=0.023) and PDGFR (P=0.022) expressions were also related to long sunitinib PFS in univariate analysis. However, the genotype did not affect either response rate or PFS of sunitinib. CONCLUSION: In conclusion, expressions of VEGF, PDGFR, and CD34 may have predictive value in sunitinib treatment.