Introduction:Gastrointestinal Stromal Tumor (GIST) is an uncommon mesenchymal tumor of the gastrointestinal tract. It is rarely presented as Multiple Primary Malignancy Syndrome (MPMS) without an association with the familial syndromes. Case Presentation: A 63-year-old Iranian Azeri man admitted to a government hospital, affiliated to the Tabriz University of Medical Sciences, Tabriz, Iran, in 2012. The illness presented with complicated gastrointestinal problems with the diagnosis of GIST of the stomach, treated with imatinib. They family history and the screening tests of malignancies were negative, but the patient diagnosed with Squamous Cell Carcinoma (SCC) of the lower lip, leading to 28 courses of radiotherapy, followed by the recurrence of gastrointestinal symptoms, the GIST and SCC of the esophagus, that was also detected accidentally. Conclusions: Management of the multiple primary malignancy syndrome needs multidisciplinary teamwork. The study of MPMs, its etiology, and epidemiology can provide us proper ways of management.