Mycotoxins are secondary metabolites produced by fungi that may contaminate different foods intended for human consumption, resulting in a widespread exposure worldwide. The novel exposome paradigm has the ambition to decipher the different environmental insults threating human health throughout the entire lifespan. Given the large potential impact of mycotoxins in terms of human exposure and related health effects, the ambition of this review is to present this group of chemical compounds and the high interest to be included in exposome projects. Furthermore, we also attempt to approach the novel exposome paradigm to more traditional disciplines such as mycotoxin exposure assessment and mycotoxicology, introducing the new methodological challenges and translational needs. Hence, we provide an overview of major biomarkers currently developed, biological matrices where these may be found, an overview of internal exposure levels and potential co-occurrence with environmental chemicals and finally an overview of major health effects with the illustrative example of the potent xenoestrogen zearalenol. Conversely, these new approaches may be an excellent opportunity to fill many research gaps on mycotoxins research as the identification of associations with human health, elucidation of join effect with other environmental exposures or the decipher of underlying molecular mechanisms by using advanced OMICs technologies.