In the years 2006-2008 the effects of two cultivation systems (conventional and ecological) on the number of yeasts and mycelial fungi on grains ofwinter wheat cultivars: Roma and Żyta (in 2006 and 2007), as well as cultivars Legenda and Bogatka (in 2008) were studied. Quantitatively populations of these microorganisms on winter wheat grain were in most cases not significantly differentiated under the compared systems. The dominating genera within mycelial fungi were: Cladosporium, Fusarium and Altemaria. Moreover, qualitative analyses of mycelial fungi have shown that grains ofwinter wheat under the ecological system were in a lower extent colonized with Fusarium species than grains under the conventional system. Fusarium poe was most frequently isolated from the studied grain, while Fusarium sporotrichioides and Fusarium tricinctum were rare.