Inclusion Criteria

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