Introduction The occurrence of synchronous or metachronous malignant epithelial and mesenchymal tumors is rare. Infiltrating ductal breast cancer rarely produces metastasis in the gastrointestinal tract, and when it does, it represents a significant differential diagnostic problem. Morphologically, they can mimic primary cancers localized in the gastrointestinal tract or peritoneum. Case outline In this paper, we present a female patient with primary, synchronous bilateral breast cancer, which after five years of follow-up had given metastases to the lungs, bones, peritoneum and mesentery, and in a node localized in the small intestine. The node was composed of two malignant components-a mesenchymal one and an epithelial one. The mesenchymal component had histologic and immunophenotypic characteristics of a gastrointestinal stromal tumor and the epithelial component was morphologically and immunohistochemically identical to the diagnosed primary breast cancer. Because of all this, the nodal tumor mass was interpreted as a primary gastrointestinal stromal tumor of the small intestine, in which the deposit of metastatic ductal breast carcinoma was observed. Conclusion Metastases of breast cancer in organs of the gastrointestinal tract are encountered rarely, mainly in the terminal stage of the disease. In available literature, a case of metastasis of breast cancer (metastasis of malignant epithelial tumors) in gastrointestinal stromal tumor has not been found.