Paragangliomas are rare tumours originating from neuroectodermic remnants and are usually considered as benign. We present two cases of paraganglioma of the ampulla of Vater that were treated surgically by pancreaticoduodenectomy. In one case, histopathology revealed malignant characteristics of the tumour with invasion of the pancreas and simultaneous duodenal lymph-node metastases. Both patients had a favourable outcome without disease recurrence at 40 and 44 months postoperatively. Only 21 cases of ampullary paraganglioma have been reported in the literature, 7 of them with malignant characteristics. In conclusion, paragangliomas of the ampulla of Vater have malignant potential. Surgical therapy of these tumours should not be limited to local resection, as disease recurrence and lymph node involvement have been reported. We propose that paragangliomas of the ampulla of Vater should be operated by cephalic pancreaticoduodenectomy, which allows long-term and disease-free survival.