AbstractLough Neagh is home to the largest wild‐caught European eel (Anguilla anguilla) commercial fishery in the EU, producing 14% of the EU catch and worth £3.2 million to the local economy. Viral infections have been suggested to play a contributory role in the decline of the worldwide eel stock, but previous studies of the Lough Neagh European eel population had not observed either acute or chronic viral signs. Eel virus European (EVE), Eel virus European X (EVEX) and Anguillid herpesvirus‐1 (HVA) have been detected throughout Europe and as the Lough Neagh eel fishery is supplemented by re‐stocking of eels from France, Spain and the United Kingdom and these viral infections may be asymptomatic, it is vital that the viral pathogen prevalence in the Lough is accurately determined. This study aimed to ascertain the presence of these viruses in the Lough Neagh European eel population by employing novel molecular techniques testing specifically for the presence of EVE, EVEX and HVA. No evidence was found of HVA infection, whereas EVE and EVEX were found, albeit at a very low prevalence.