Although apoptosis (programmed cell death type I) is more frequently reported in the literature in imatinib-treated gastrointestinal stromal tumor (GIST) cell lines,morphological features consistent with autophagic changes aremore often encountered in surgical specimens of treated patients. Autophagy (programmed cell death type II) is highly regulated by a tumor-suppressor mechanism that mainly involves the genes beclin1, PI3KIII, and bcl2. Being our material not suitable for electron microscopy analysis (not paraformaldehyde-glutaraldehyde-fixed), we evaluated the morphological, biochemical, and immunophenotypical profiles expected to be related to autophagy and apoptosis in a series of surgically resected samples taken from 11 imatinib-treated patients with molecularly characterized GISTs. The samples were examined for imatinib-induced morphological changes, the presence/interactions of the autophagic-related proteins (beclin1, PI3KIII, bcl2, and LC3-II) and the presence of apoptosis-related proteins (caspase 3, caspase 7, and lamin A/C) by means ofWestern blot analysis and coimmunoprecipitation, complemented by immunohistochemistry. We also studied samples of two untreated GISTs used as controls. Sampling areas with different residual cellularity scores fromboth the imatinib-treated and untreated patients showed biochemical and immunohistochemical evidence of high levels of proautophagy beclin1/PI3KIII and low levels of antiautophagy beclin1/bcl2 complexes, together with the presence of LC3-II detected by Western blot analysis, thus supporting the presence of autophagy. There was no expression of cleaved/activated caspase 3 or 7 or cleaved lamin A/C. Our descriptive results support the idea that GISTs activate autophagy rather than apoptosis in response to imatinib treatment and that their molecular makeup includes fingerprints of autophagy.