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....In summary, anlotinib showed moderate antitumor activity in drug-resistant GIST cell lines in vitro, and acceptable PFS and good tolerance were obtained in this prospective study.