Fungal mycotoxins of the genera Aspergillus, Fusarium, and Penicillium contaminate feedstuff and food to induce serious health issues in humans and animals known as mycotoxicosis. Mycotoxins of Aspergillus, Penicillium, Alternaria, and Fusarium are serious threats to food quality and safety. Aflatoxins, zearalenone, ochratoxins, patulin, fumonisins, trichothecenes, deoxynivalenol has been documented to exert nephrotoxicity, immunotoxicity, hepatotoxicity, carcinogenicity, teratogenicity, and neurotoxicity in animals and humans. Implementation of HACCP-based methods can mitigate mycotoxin-linked contamination whereas traditional methods (physical, biological, and chemical) can facilitate the decontamination process. However, increasing fungal resistance and challenges associated with conventional systems require innovative strategies to rapidly eliminate mycotoxins without affecting the quality. The most important food-contaminating mycotoxins include liver-damaging aflatoxins; kidney-damaging ochratoxin A; cancer-causing, liver-damaging, and developmental defects-associated fumonisins; acute cardiac damage-related moniliformin; and gastroenteritis and immunotoxicity-associated zearalenone and deoxynivalenol. Therefore, mycotoxins can be classified as teratogens, hepatotoxins, allergens, nephrotoxins, mutagens, neurotoxins, immunotoxins, and carcinogens. Mycotoxins are associated with various animal and human diseases including porcine pulmonary edema, Reye’s disease, Balkan endemic nephropathy, equine leuko-encephalomalacia, and alimentary toxic aleukia of humans. This study discusses the individual and combined effects of foodborne fungal mycotoxins along with the associated biochemical mechanisms and pathologies.