Wegener's granulomatosis is a systemic vasculitis with prominent involvement of the respiratory tract and kidney. There are 10 patients with Wegener's granulomatosis in the literature who were documented as acute pancreatitis. We present two cases with Wegener's granulomatosis presenting with acute pancreatitis and pancreatic pseudocyst. Endosonography-guided drainage of the pancreatic pseudocyst led to rapid clinical improvement. Pancreatic pseudocyst in Wegener's granulomatosis is not reported in the literature, and these are the first cases of Wegener's granulomatosis to be managed by endosonography-guided cyst drainage. The safety of endosonography-guided pancreatic pseudocyst drainage and the clinical features of the previous Wegener's granulomatosis cases with acute pancreatitis are discussed.