Gastrointestinal stromal tumor (GIST) is an uncommon mesenchymal tumor, and has been shown to be associated with synchronous or metachronous second malignancies. Rare cases of coincident GIST and non-Hodgkin lymphomas (NHL) have been reported previously. Here, we report two cases of GIST and coincident primary breast lymphoma, an uncommon subtype of extranodal NHL. We propose that the exceedingly low likelihood of both these cancers occurring in these two patients by chance warrants examination for possible common oncogenic pathways in these lesions, possibly involving shared anti-apoptotic mechanisms. Further research is vital to elucidate common oncogenic pathways between such rare lesions.