Background: Limited data exist on the combined use of EUS-guided FNA (EUS-FNA) and flow cytometry (FC) in the diagnosis of lymphoma. The aim of this study was to evaluate the accuracy of EUS-FNA combined with FC in the diagnosis of primary or recurrent lymphoma. Methods: This study was a retrospective analysis of a prospective collection of data over a 3-year period. Over 3 years, 29 patients with lesions (n = 31) suspicious for lymphoma underwent EUS-FNA and FC. Results: Of the 29 patients, 10 patients had lymphoma and 17 patients had nonlymphoma lesions; for two patients, final diagnosis was indeterminate because of insufficient material for FC. The lymphoma cases included non-Hodgkin's lymphoma (n = 6, including 3 recurrences), mucosa-associated lymphoid tissue (MALT) lymphoma (n = 2), a non-GI lymphoma with mediastinal lymphadenopathy (n = 1), and an uncharacterized lymphoma (n = 1). Of the 31 lesions, 8 were true positive, 18 were true negative, and 3 were false negative; for two lesions, we could not determine the final diagnosis. No false-positive results were encountered. The sensitivity, the specificity, and the accuracy of EUS-FNA combined with FC for diagnosing lymphoma were 72.7%: 95% CI [43.3%, 90.3%], 100%: 95% CI [82.4%, 100.0%], and 89.7%: 95% CI [73.6%, 96.4%], respectively. Limitations to this study include a short duration of follow-up and a lack of a surgical criterion standard. Conclusions: EUS-FNA in combination with FC allows the diagnosis of primary suspected or recurrent lymphoma. It also is an adjunct in staging MALT lymphoma and could direct clinicians toward further investigative procedures. Copyright © 2005 by the American Society for Gastrointestinal Endoscopy.