Objective: Gastrointestinal stromal tumor (GIST) is one of the most common mesenchymal tumors in the gastrointestinal system, occurring frequently after epithelial tumors. Although rare, secondary epithelial malignancies can be associated with GISTs. It was planned to conduct a retrospective cohort study evaluating the coexistence of GISTs with malignancies and their long-term outcomes through clinical and pathological findings. Material and Methods: Demographic and clinicopathological data of 69 patients who underwent surgery for GIST between January 2011 and November 2021 were retrieved from the patient database. Variables between the groups with only GIST and those with a secondary malignancy alongside GIST were analyzed using the Chi-square test and Mann-Whitney U test. Long-term survival analyses were conducted using the Kaplan-Meier test. A p-value of <0.05 was considered statistically significant. Results: Out of the 69 patients in our population, 40 (58%) were male, and the median age was 65 years (interquartile range= 56-75). GIST was the most commonly located in the stomach (59.4%), and nine (13%) patients had a secondary malignancy. Tumor size, smooth muscle antibody (SMA), and S100 antibody expression showed significant differences between the groups (p< 0.001, p= 0.015, p= 0.006). Shorter survival was observed in patients with GIST plus secondary malignancy (p= 0.005). Conclusion: The incidence of other intraabdominal malignancies occurring alongside GISTs is more common than have been previously thought. While the presence of a secondary malignancy does not impact the overall survival (OS) in GISTs, it was observed that survival is dependent on the primary malignancy. Patients diagnosed with GISTs require thorough investigation and close monitoring for secondary malignancies.