In this study, the occurrence of Fusarium mycotoxins deoxynivalenol (DON), zearalenone (ZEA) and fumonisins (FUM) was investigated in a total of 257 samples of unprocessed cereals (maize, wheat and barley), sampled annually in Bosnia and Herzegovina throughout the 2013-2015 harvesting period. The levels of mycotoxins were determined using a validated ELISA method. The results showed maize to be the most contaminated cereal among the three, with DON detected in 85%, ZEA in 73% and FUM in 67% of samples, the mean concentrations of the toxins observed during the study period thereby being 984±957 μg/kg, 326±314 μg/kg, and 1,259±1,161 μg/kg, respectively. Twenty samples (7.8%) were proven inadmissible for consumption as foodstuffs (Commission Regulation 1881/2006), and 3 samples (1.2%) were proven inadmissible even as feedstuffs (Commission Recommendation 2006/576/EC). Significantly higher (p < 0.05) mycotoxin levels determined in samples harvested in 2014 as compared to those harvested in 2013 and 2015 could be associated with heavy rainfall periods witnessed in 2014 that could favour the formation of moulds, and consequently also the increased production of Fusarium mycotoxins.