(1) Background: Food and feed safety legislation does not concern all the mycotoxins generated by Penicillium and Aspergillus spp. Certain mycotoxins, including mycophenolic acid (MPA), cyclopiazonic acid (CPA), penicillic acid (PA), roquefortine C (ROQ C), and gliotoxin (GLI), are regarded as having lower toxicity levels, and hence are not included in food and feed legislation. It is obvious that xenobiotics, including mycotoxins, exert synergistic harmful health effects on human and animal when exposed through food and feed. (2) Methods: The presence of these substances in maize and wheat grown in Albania across two consecutive harvesting seasons was investigated by liquid chromatography and mass spectrometry (LC-MS/MS). (3) Results: The findings indicated the presence of these mycotoxins in maize grain but not in wheat grain. In the 2014 season, they exhibited a higher contamination incidence than in the 2015 season. The most commonly detected mycotoxin was MPA, followed by CPA and ROQ C toxin, while PA and GLI were not detected. The MPA revealed a concentration range of 72.9–3447 μg/kg, with a mean value of 1064 μg/kg. Mycophenolic acid was detected in the maize samples collected during the 2015 season. (4) Conclusions: These findings suggest that focusing the investigation only on “controlled” mycotoxins will not produce a proper risk assessment and may not adequately address the possible harmful impacts of mycotoxins on human and animal health due to mycotoxins’ co-occurrence.
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