In May 2014, catastrophical floods have devastated eastern areas of Croatia, particullarly village Gunja. Flood waters may bring feces, bacteria, and fungi; change composition of soil on which crops are cultivated, but also change moisture levels. For this reason, samples of cereals have been collected from areas of Gunja; and Gornji Stupnik as control. Colonies that grew on appropriate culture media were identified by comparing their morphological features with data from literature. Average concentration of fungi in samples from Gunja is calculated at 5,1 x 105 CFU/g, which is statistically a significant increase compared to average concentration in samples collected in Gornji Stupnik (7,3 x 103 CFU/g)(p=0,0286). Most numerous fungal genera were Cladosporium, Fusarium and Penicillium. Fusarium spp. were found in all the samples collected in Gunja, Cladosporium spp. were found only in oat samples, and Penicillium spp. appeared in all the samples but one. Fusarium spp. were especially dominant in corn. Cladosporium spp. were prevalent at Gornji Stupnik area. Alternaria spp., Mucor spp. and Phoma spp. were found in isolated cases. Aspergillus spp. were found in 2 samples collected at control site. Fusarium genus is one of the main producers of mycotoxins – mostly trichothecens, fumonisins and zearalenone. Chronic exposure to mycotoxins can have a serious impact on human and animal health.