Specific inhibitors can be designed to inactivate the molecular pathways involved in tumor growth. A compelling example is the use of small molecule drugs, such as imatinib (Gleevec), which inhibit the KIT tyrosine kinase in gastrointestinal stromal tumors (GIST). Assays are needed to determine which inhibitor is most effective at silencing the KIT kinase in each GIST patient. The aim of this study was to develop a robust, cytology-based assay to measure tumor susceptibility to target-specific small molecule inhibitors. We created an immortal GIST cell line (GIST882) that was treated in vitro with several inhibitors of the KIT --> AKT --> mTOR --> S6 signaling pathway. KIT was inhibited with imatinib, and mTOR with RAD001. Treatment response was assessed in cytologic preparations by immunocytochemical staining with antibodies to KIT, phospho-KIT, phospho-AKT, and phospho-S6. Optimization was performed to maximize staining in the absence of inhibitor, and minimize staining in the presence of inhibitor. GIST882 cells demonstrated strong, robust phospho-S6 expression in the absence of inhibitor. This expression was completely inhibited by treatment with upstream signaling pathway inhibitors (imatinib and RAD001). Other phospho-specific antibodies had weaker baseline reactivity in the absence of inhibitor. The accuracy of the immunocytochemical results on the cytologic preparations was validated by immunoblotting studies. Our study demonstrates the feasibility of cytologic methods to monitor labile biochemical responses in tumor cells during drug therapy. Such approaches will be enhanced by the development of additional activation state-specific antibodies, particularly those optimized for use in cytologic preparations.