Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. Significant prognostic heterogeneity has been described with GISTs, which can range from clinically benign to frankly malignant tumors. Although several GISTs classification systems have been established to identify tumors with high risk of relapse, there is a sample of patients who still do not receive an appropriate treatment. The classification scores by Fletcher et al and Miettinen and Lasota are the most widely clinically accepted, while the Memorial Sloan Kettering Cancer Center prognostic nomogram is considered the most feasible. There are several studies about new prognostic factors in radiological, biological, and surgical fields. Tumors with mixed growth pattern, enlarged vessels feeding, or draining the mass on computed tomography or with high standardized uptake values on positron emission tomography/ computed tomography should be considered as high-grade GISTs. Among biological markers, the most relevant are programmed cell death ligand 1, Pfetin, SETD2, SLITRK3, mir-215-5p, and monoglyceride lipase. These factors need to be further investigated in order to validate their use in risk stratification. Laparoscopy and open surgery can have the same oncological outcomes even for larger gastric tumors, up to 10 cm. Laparoscopy should be considered the best surgical approach when executed by skilled surgeons and for tumor localized in reachable sites. Adjuvant chemotherapy with imatinib is recommended for high-grade GIST, but the optimal duration of this therapy is still debated. Some authors advocated that imatinib treatment should last for 5 years. A subgroup of GIST is represented by small GISTs, lesions <2 cm in diameter, which need a radical surgical treatment in the presence of symptoms or when high-risk factors such as irregular borders, cystic spaces, ulceration, echogenic foci, internal heterogeneity, tumor progression during follow-up, small intestinal or colorectal localization are present.