Objectives: Thoracic and abdominal lymph nodes may be enlarged in a variety of disorders. Endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) is a well-established technique for sampling such nodes, but samples obtained are small, which may make definitive diagnosis difficult. We conducted a retrospective review to determine the contribution of ancillary techniques, such as special histochemistry (SHC), immunohistochemistry (IHC) and flow cytometry, in increasing the diagnostic yield of EUS-FNA carried out at our institution. Study Design: Between November 2005 and December 2012, 278 patients underwent EUS-FNA of enlarged thoracic and abdominal nodes at our institution. All specimens obtained were subjected to rapid on-site evaluation. Data were reviewed in all patients requiring ancillary techniques for definitive diagnosis. Results: Ancillary techniques were performed in 111 of 278 cases. IHC was performed in 24, flow cytometry in 3 and SHC staining in 84. IHC and SHC aided in reaching a definitive diagnosis in 19 of 24 and 3 cases, respectively. Flow cytometry led to a definitive diagnosis in 3 cases. A total of 80 cases were also submitted to culture for tuberculosis with 6 positive for Mycobacterium tuberculosis. Conclusions: Ancillary studies in EUS-FNA of thoracic and abdominal lymph nodes can significantly improve the yield of EUS-FNA.