Exposure assessment in epidemiological studies remains as a key bias domain, prompting for reliable and accurate methods reflecting the true individual exposure. For that reason, the use of exposure biomarkers has become the gold-standard method for environmental chemicals and food contaminants in epidemiology. In the last few years, a growing list of biomonitoring studies has revealed the widespread exposure of population to mycotoxins, mainly aflatoxins, ochratoxins or trichothecenes, subject to geographical localisation. Despite the advances in mass-spectrometry, mycotoxins remain largely overlooked by mainstream epidemiological research. To date, the scarce epidemiological evidence has elucidated the associations between exposure to aflatoxins and hepatocellular carcinoma, cirrhosis or impairment of infant growth. The novel exposome paradigm offers a unique opportunity to boost the epidemiological research of mycotoxins. Nonetheless, there is an urgent need that mycotoxins catch the attention of mainstream epidemiological researchers, especially those intending to develop chemical agnostic approaches in pathologies and populations where mycotoxins may represent a concern.