In order to investigate the pre-harvest contamination of maize plants by Fusarium species in Belgium, a three-year survey has been performed in five fields in which three hybrids differing in susceptibility to maize stalk rot were sampled at four different physiological stages. An extensive collection of 5,659 Fusarium isolates characterized at the species level was established during the 2005, 2006, and 2007 growing seasons, with a total of 23 different Fusarium species identified to occur on ears and stalks. A high number of plants was already contaminated by Fusarium spp. at the anthesis stage, although no symptoms were visible on ears or on stalks. As the season progressed, the incidence of Fusarium-infected maize plants reached 100% in several fields. At the end of the growing season, the most frequently isolated species in maize ears were F. graminearum, sometimes associated with F. avenaceum, F. crookwellense, F. culmorum, F. poae, and F. temperatum, a new species recently described on maize. The predominant Fusarium species detected in stalks at the end of the growing season were F. graminearum and F. crookwellense, often associated with F. culmorum and F. temperatum. Year-to-year variability observed for the incidence of F. graminearum can most likely be associated with differences in climatic conditions among the three years.