We intended to find predictive markers in advanced gastrointestinal stromal tumor patients treated with sunitinib. Korean patients who received sunitinib after imatinib failure for advanced gastrointestinal stromal tumor were studied. Genotyping for KIT and PDGFRA were performed. An immunohistochemical stain for PDGFR-α, PDGFR-β, and vascular endothelial growth factor (VEGF) was performed. A total of 22 patients were analyzed. Their median age was 55.1 years, and the male to female ratio was 12:10. The response rate of sunitinib was 30.4% and the median progression-free survival (PFS) was 10.1 months. In the 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 the PFS of sunitinib. In conclusion, expressions of VEGF, PDGFR, and CD34 may have predictive value in sunitinib treatments.