Objective To describe pharmacokinetic of imatinib in a cohort of gastrointestinal stromal tumor (GIST) patients in routine clinical care from West China Hospital of Sichuan University. Methods The imatinib trough concentration (Cmin) in 42 patients with GIST who were taking imatinib in routine clinical care setting in West China Hospital from 2010 to 2016 was measured. The clinical features and follow-up data were collected. Results The mean imatinib Cmin in 42 patients was 1 757 μg/L (199–7 435 μg/L), 10 of 42 patients presented with Cmin values was lower than 1 000 μg/L. The imatinib Cmin of 18 patients received an imatinib dose of 300 mg/d or 24 patients treated with 400 mg/d imatinib was (1 313±479) μg/L and (1 775±1 520) μg/L, respectively (P=0.222), but the rate of low Cmin (lower than 1 000 μg/L) in the two different dose groups had no significant difference (P=0.347). In Cox regression, no statistically significant association between the low Cmin and the time to progression of GIST could be demonstrated 〔HR=0.171, 95%CI：(0.106, 12.990),P=0.898〕. Conclusion The preliminary results of limited cases in this study show that some GIST patients are systematically underexposed in routine clinical care, an individualized treatment based on monitoring of imatinib Cmin is likely to be more efficient than a fixed-dose treatment.