Gastrointestinal stromal tumors are the most common mesenchymal tumors in the abdomen and occur in Germany with an incidence of 10 to 15 cases per million inhabitants. Clear identification and characterization are of major importance for the prognosis and therapy of patients. Similarly, they have to be differentiated from other mesenchymal neoplasias such as leiomyomatous, neurogenic, adipocytic, and fibroblastic tumors. Additionally, the number of translocation positive neoplasias is increasing, requiring the use of adequate molecular assays. The aim of this paper is to give practical advice for their identification. Reference pathology is one possibility to support the correct diagnosis.