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Introduction: Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of the gastrointestinal tract. GIST has been shown to over-express c-KIT (CD117), the receptor tyrosine kinase. Imatinib (STI571 or Glivec) is a new type of tyrosine kinase inhibitor that selectively inhibits various tyrosine kinases and has been successfully used to treat GIST. In this study we have compared the results of F-18 FDG PET with those of CT in patients with GIST before and early after the treatment with Imatinib. Methods: The performance of CT and FDG PET imaging in the staging and follow-up of GIST lesion was retrospectively evaluated and compared in 15 patients with 67 suspicious lesions. All patients were examined before and after treatment with Imatinib. Findings of CT and FDG PET were compared on both patientand lesion-based basis for the whole group and for anatomic locations. Results: Overall 67 lesions were detected in both pre-therapeutic FDG PET and CT imaging. In the pre-treatment studies there was no significant difference between detected lesions on FDG PET and CT (p = 0.19). However, after treatment with Imatinib (follow-up interval of 30 + 16 days), FDG PET predicted response to therapy earlier than CT in 18% of lesions and 14% of patients, respectively. There was no significant difference in the density of malignant lesions by means of Hounsfield unit (HU) in the baseline PET in comparison to the early post-therapeutic investigations (93 + 16 vs. 90 + 22). Conclusion: For treatment monitoring of Imatinib in GIST patients, FDG PET gives more precise information of active state of disease compared with CT.