Gastrointestinal stromal tumors (GISTs) constitute an important group of mesenchymal tumors of gastrointestinal tract. Sporadic coexistence of papillary renal cell carcinoma and gastrointestinal stromal tumor is known. Mutation in proto-oncogenes, related to tyrosine kinase receptor molecules are involved in both tumors. We here in present a case of conventional clear cell renal cell carcinoma in a patient diagnosed to have gastrointestinal stromal tumor on endoscopic biopsy, stomach. It would be interesting to verify our case with findings of larger cancer registries. The repeated associations of specific tumors often serve as pointers to novel oncogene defects. Such germ line mutations are rarely found in sporadic cases such as ours.