PURPOSE: Systemic inflammation and immune response are associated with tumors'prognosis. However, there is little information about inflammatory indexes in patients with gastrointestinal stromal tumor (GIST). In this study, we aimed to determine the prognostic significance of inflammation indexes such as neutrophil to lymphocyte ratio (NLR), systemic immune-inflammation index (SII), prognostic nutritional index (PNI) and Glasgow prognostic score (GPS) in GIST patients. METHODS: Forty-five patients diagnosed with GIST between 2003 and 2018 were included in the study. The effects of NLR, SII, PNI and GPS on progression-free survival (PFS) and overall survival (OS) estimated based on clinicopathological and laboratory data were evaluated by Kaplan-Meier and Cox regression analysis. RESULTS: The optimal cut-off values for NLR, SII and PNI were 2.54, 940, and 37.5, respectively. Low SII and higher PNI values were associated with longer PFS (p=0.041, p=0.018, respectively). In terms of OS, patients with high NLR, high SII and low PNI had a shorter lifespan. In multivariate analysis, only SII was found to be independent prognostic factor. CONCLUSION: In cases with GIST, SII may predict recurrence and survival.