DISEASE CHARACTERISTICS:

• Biopsy proven gastrointestinal stromal tumor

• Patients previously treated with imatinib mesylate must have documented progression of disease

  • Untreated disease allowed
• Must have ≥ 1 measurable lesion by RECIST
• No history of or known brain metastases, spinal cord compression,carcinomatous meningitis, or evidence of symptomatic brain or leptomeningeal disease on screening CT or MRI scan

PATIENT CHARACTERISTICS:

• ECOG performance status 0-2
• ANC ≥ 1,500/μL
• Hemoglobin ≥ 9.0 g/dL
• Platelet count ≥ 150,000/μL
• Total serum bilirubin ≤ 2.0 mg/dL
• Serum calcium ≤ 12.0 mg/dL
• Serum creatinine ≤ 1.8 mg/dL
• AST and ALT ≤ 3 times upper limit of normal (ULN) (5 times ULN if liver function abnormalities are due to underlying malignancy)
• Able to take oral medications
• Not pregnant or nursing
• Negative pregnancy test
• Fertile patients must use effective contraception
• No grade 3 hemorrhage within the past 4 weeks
• No myocardial infarction, severe or unstable angina, coronary or peripheral artery bypass graft, symptomatic congestive heart failure, cerebrovascular accident or transient ischemic attack, or pulmonary embolism within the past 6 months
• No ongoing cardiac dysrhythmias ≥ grade 2
• No prolonged QTc interval on baseline EKG
• No hypertension that cannot be controlled by medications (BP > 150/100 mm Hg, despite medical therapy)
• No pre-existing thyroid abnormality with thyroid function that cannot be maintained in the normal range with medication
• No known HIV or AIDS-related illness or other active infection
• No other severe, acute, or chronic medical or psychiatric condition or laboratory abnormality that may increase the risk associated with study participation or study drug administration, or may interfere with the interpretation of study results, and in the judgment of the investigator, preclude study entry
• No malabsorption syndrome
• No prior intolerance of imatinib mesylate or toxicity necessitating dose modification
• No prior intolerance of sunitinib malate or toxicity necessitating dose modification

PRIOR CONCURRENT THERAPY:

• Recovered from all acute toxic effects of prior chemotherapy, radiotherapy, or surgical procedures
• No major surgery or radiotherapy within the past 4 weeks
• No concurrent treatment on another clinical trial, except supportive care trials or non-treatment trials (e.g., quality of life)
• No concurrent ketoconazole and other agents known to induce CYP3A4
• No concurrent theophylline or phenobarbital and/or other agents metabolized by the cytochrome P450 system
• No ongoing therapeutic doses of coumadin, except low-dose oral coumadin up to 2 mg once daily for thrombosis prophylaxis
• No concurrent Hypericum perforatum (St. John's wort) or other herbal medications