Gastrointestinal stromal tumors (GISTs) are rare neoplasms, but they also represent the most common mesenchymal tumors of the gastrointestinal tract originating from the cell of Cajal. GIST incidence ranges around 1% of all gastrointestinal malignancies. Approximately 5% of all GISTs have a hereditary etiology. The remaining 95% of GISTs are considered sporadic events, with up to 75% of cases driven by a constitutional activation of the c-KIT proto-oncogene. GISTs are generally solitary lesions. Nonetheless, multiple sporadic GISTs can occur and present as synchronous or metachronous tumors, usually associated with familial GIST. Here, we report a case of primary prostate and lung tumors associated with gastric and small bowel GISTs, unrelated to any known hereditary syndrome. Also, in the case we describe, the prostatic tumor came before the GISTs, while the lung tumor occurred later in time and led to pulmonary lobectomy plus lymphoadenectomy, with a diagnosis of nonsmall cell lung cancer. With the exception of a slight difference in lymphoid infiltration, the abdominal and gastric GIST nodules shared the same proliferative MIB1 index and mitotic count. However, the genetic analysis revealed that the gastric GIST and abdominal tumors were characterized by two different c-KIT mutations. This molecular heterogeneity supported the hypothesis of two different synchronous GISTs arising from stomach and ileum. At present, the patient is disease free and has already completed the third year of adjuvant therapy with imatinib. This case supports the importance of the analysis of c-KIT mutational status to distinguish metastases from synchronous multicentric GISTs, with relevant implications in therapeutic decisions, as well as the importance of a dedicated multidisciplinary team and of a radiological follow-up after the diagnosis of a primary GIST, to discover a relapse of the GIST or, possibly, additional malignancies.