We tested the inhibitory effect of anlotinib in GIST cell lines with different gene mutations and evaluated the efficacy of anlotinib for patients with metastatic GIST….Seven patients had partial response and 39 patients had stable disease. The median PFS was 8.0 months....The median PFS of patients in KIT exon 9 mutation (n = 5), KIT exon 11 mutation (n = 37), and wild type (n = 11) subgroups were 2.0 months (95% CI, 1.2-8.4), 8.0 months (95% CI, 4.6-11.4), and 9.5 months (95% CI, 0.0-24.1), respectively. The median PFS of secondary exon 17 mutation (n = 3) treated with anlotinib was 2.5 months (95% CI, 1.217-3.783). The PFS of 2 patients with V654A secondary mutation treated with anlotinib were 3.5 and 5.0 months, respectively.