Although a broad range of pancreatic, gastrointestinal, thoracic, and abdominal pathology may be sampled by endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA), certain difficulties tend to recur because of the frequency of certain sample types and because of the nature of their individual cytomorphologic profiles. With this in mind, we review certain pitfalls that may befall cytopathologists with EUS-guided FNA. We discuss the diagnosis of pancreatic ductal adenocarcinoma and of other pancreatic epithelioid tumors including pancreatic endocrine neoplasms, solid pseudopapillary tumors, and acinar cell carcinomas. We also discuss the diagnosis of pancreatic cystic neoplasia including intraductal papillary mucinous neoplasms and mucinous cystic neoplasms and the diagnosis of gastrointestinal mesenchymal neoplasia with particular attention to gastrointestinal stromal tumors. Finally, we discuss the interpretation of lymph node aspirates.