Gastrointestinal stromal tumors (GIST) contain tumor-infiltrating immune cells and their presence provides an opportunity and rationale for developing effective forms of immunotherapy. The types of tumor-infiltrating inflammatory cells and relevant immune checkpoint inhibitors are the focus of active investigation. The most numerous tumor-infiltrating inflammatory cells are tumorassociated macrophages (TAMs) and CD3+ T cells. Studies have shown that patients with GISTs that harbor increased numbers of CD3+ T cells have better outcomes. However, the clinical behavior of GIST has not been shown to correlate with the number of TAMs. The biological significance of other less frequent tumor-infiltrating immune cells including tumor-infiltrating neurtrophils (TINs), natural killer cells (NKs), B cells, dendritic cells (DCs) remains unclear. The immune checkpoint inhibitors CTLA-4, PD1/PDL1 and TIM3/galectin-9 are molecules that can be targeted by synthesized antibodies. Clinical and pre-clinical trials using this approach against immune checkpoint inhibitors, anti-KIT antibody and the generation of chimeric antigen receptor (CAR) T-cells have shown promising results. The treatment of GIST with immunotherapy is complex and evolving; this article reviews its current status for patients with GISTs.