Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors that represent the second most common type in the gastrointestinal system, but clinical outcomes vary due to complex molecular changes. The aim of our study is to highlight a unique case of a 5th decade male, presenting a double primary GIST of the jejunum, associated with a rare immunophenotype and with a high risk of malignancy. Ancillary studies were performed using several biomarkers [cluster of differentiation (CD) 117∕c-kit, discovered on GIST1 (DOG1), desmin, S-100, vimentin, cytokeratin 7 (CK7), Ki67, actin, platelet-derived growth factor receptor alpha (PDGFRA) and CD34], in order to confirm the diagnosis and to evaluate prognostic and predictive factors. A KIT-negative∕PDGFRA-positive immunophenotype was obtained in our case and it was associated with a poor prognosis. Its unfavorable clinical evolution was sustained by recurrence as malignant (GIST) with dedifferentiation and metastases developed in less than one year after the initial diagnosis. Clinico-morphological features of GISTs with an impact on survival must be identified and a tailored therapy should be applied for each case.