This study aimed to assess post-harvest contamination with mycotoxins in the context of the geographic and agroclimatic conditions in Romania in 2012–2015, a period that was characterized by extreme meteorological events and the effects of climate change. The samples were randomly sampled from five agricultural regions of Romania and analyzed for mycotoxins by enzyme-linked immunosorbent assay. An SPSS analysis was done to explore correlations between mycotoxins (deoxynivalenol—DON, aflatoxins—AF, ochratoxin A—OTA, zearalenone—ZEA), product types (raw cereal, processed cereal, cereal-based food), geographic coordinates (latitude, longitude, agricultural region), and agroclimatic factors (air temperature, precipitation, soil moisture reserve, aridity index, soil type). In the southeast part of the Southern Plain and Dobrogea (Baragan Plain, located at 44–45° N, 26–27° E), contamination with AF and OTA was higher in raw and processed cereals (maize in silo, silo corn germs) in the dry years (2012 and 2013), and contamination with DON was high in processed cereals (wheat flour type 450) in the rainy year (2014). DON and OTA contamination were significantly correlated with cumulative precipitation in all years, while AF and ZEA contamination were non-significantly correlated with climatic factors and aridity indices. The distribution of mycotoxins by product type and the non-robust correlations between post-harvest mycotoxins and agrometeorological factors could be explained by the use of quality management systems that control cereal at warehouse receptions, performant processing technologies, and the quality of storage spaces of agri-food companies. The Baragan Plain is Romania’s most sensitive area to the predicted climate change in southeast Europe, which may be associated with its increased cereal contamination with AF and OTA.
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