Fusarium mycotoxins, such as fumonisins, trichothecenes, zearalenone and emerging fusariotoxins, common contaminants of feed and food, have received increased interest, due to the possible impact on animal and human health. In this context, it is urgent to focus our attention on fusariotoxins adverse effects, considering and analysing data in relation to their species-specificity. The in vitro approach for fusariotoxins risk assessment evaluation, through porcine epithelial barriers model, allowed to collect information on their absorption profile, bioavailability and toxicity. The aim of this review is to give an overview on Fusarium mycotoxins and their interactions with porcine intestinal and brain in vitro barriers, because they represent direct target organs of toxicity and as tools to evaluate their permeability and transport.