Potato virus Y (PVY), one of the most important agents causing potato crop losses worldwide, is transmitted by a variety of aphid species in a non-persistent manner. Several PVY strains have been differentiated, all of them causing different symptoms and symptom expression levels on numerous commercial potato cultivars. In Belgium, strains belonging to the N group have been reported as the most prevalent, but no detailed information on the relative importance of the PVY strains in Belgium have been published to date. We report here on a survey performed on Belgian seed potatoes harvested in 2010 in which 2700 individual tubers from 54 seed potato lots originating from 54 farms were screened for presence of PVY. The results revealed a high PVY incidence and substantial strain diversity in some farms. The dominance of the N group in Belgian seed potatoes was confirmed, while the 0 strain was only found in a few locations. Further characterization using multiplex PCR identified 75% of the isolates as NTN strains and 7.5% as Wilga strain (N-Wi). The presence of the N-Wi strain was confirmed and characterized for the first time in Belgian seed potato production.