Systemic inflammation and immune response were associated with prognosis of tumors. However, data was limited due to the relatively low incidence of gastrointestinal stromal tumors (GISTs). The aim of the present study was to investigate the predictive value of preoperative peripheral blood cells in prognosis of GISTs.From September 2008 to July 2015, a total of 274 GIST patients in our department were enrolled in the present study. Clinicopathological features of GISTs were recorded. The association between preoperative peripheral blood cells and prognosis of GISTs were analyzed.Tumor location, tumor size, mitotic index, intratumoral necrosis, and National Institutes of Health (NIH) risk category were associated with prognosis of GISTs. High neutrophil-to-lymphocyte ratio (NLR), monocyte-to-lymphocyte ratio (MLR), platelet-to-lymphocyte ratio (PLR), neutrophil-to-white blood cell ratio (NWR), monocyte-to-white blood cell ratio (MWR) and low lymphocyte-to-white blood cell ratio (LWR) was associated with poor prognosis of GISTs (76.2% vs 83.7%, P = 0.010. 70.5% vs 98.7%, P = 0.000. 65.7% vs 96.4%, P = 0.004. 78.5% vs 82.5%, P = 0.044. 73.5% vs 97.8%, P = 0.004. 76.6% vs 83.6%, P = 0.012, respectively). However, tumor size was the only independent risk factor for prognosis according to multivariate analysis (P = 0.006). Tumor location, tumor size, mitotic index, and NIH risk category were significantly correlated with the above-mentioned parameters (all P < 0.05). The prognosis of GISTs with tumor size >5 cm, high MLR, high PLR, and high MWR was significantly lower than the remnant patients (P = 0.010).The peripheral blood routine test is convenient, reproducible, and inexpensive. High NLR, MLR, PLR, NWR, MWR, and low LWR were associated with poor prognosis of GISTs. The association between the above parameters and prognosis of GISTs may be attributed to their correlation with tumor size, mitotic index, and NIH risk category. The combination of tumor size, MLR, PLR, and MWR could further increase the predictive value of prognosis of GISTs.