We studied the use of immunocytochemical analysis with material procured by endoscopic ultrasound-guided fine-needle aspiration (EUS-guided FNA) for the diagnosis of subepithelial intramural gastrointestinal (GI) mesenchymal neoplasms (SIGIMNs). We identified all EUS-guided FNA specimens of SIGIMNs that had undergone immunocytochemical analysis. Results were compared with follow-up histologic diagnoses. There were 95 aspirates that were diagnosed as GI mesenchymal tumors (GI stromal tumors [GISTs], n = 46), leiomyomas (n = 38), peripheral nerve sheath tumors (n = 5), and other neoplasms by cytologic examination. Immunoreactivity with antibodies to CD117 always predicted GIST at follow-up; 15 of 16 cases immunoreactive with antibodies to CD34 were found to be GISTs at follow-up. Strong immunoreactivity with antibodies to smooth muscle actin or desmin usually predicted a leiomyoma at follow-up aside from a single glomus tumor and a case with apparent nonneoplastic smooth muscle contaminant. When sufficient material is present, immunocytochemical analysis used with material obtained by EUS-guided FNA is highly predictive of final pathologic diagnosis.