Cancer stem cells (CSCs) are the main cause of tumor growth, invasion, metastasis and recurrence. Recently, CSCs have been extensively studied to identify CSC-specific surface markers as well as signaling pathways that play key roles in CSCs self-renewal. The involvement of CSCs in the pathogenesis of gastrointestinal (GI) cancers also highlights these cells as a priority target for therapy. The diagnosis, prognosis and treatment of GI cancer have always been a focus of attention. Therefore, the potential application of CSCs in GI cancers is receiving increasing attention. This review summarizes the role of CSCs in GI cancers, focusing on esophageal cancer, gastric cancer, liver cancer, colorectal cancer, and pancreatic cancer. In addition, we propose CSCs as potential targets and therapeutic strategies for the effective treatment of GI cancers, which may provide better guidance for clinical treatment of GI cancers.