The mycotoxin deoxynivalenol (DON) contaminates agricultural commodities worldwide, posing health threats to humans and animals. Associated with DON are derivatives, such as deepoxy-deoxynivalenol (DOM-1), produced by enzymatic transformation of certain intestinal bacteria, which are naturally occurring or applied as feed additives. Using differentiated porcine intestinal epithelial cells (IPEC-J2), we provide the first multi-parameter comparative cytotoxicity analysis of DON and DOM-1, based on the parallel evaluation of lysosomal activity, total protein content, membrane integrity, mitochondrial metabolism and ATP synthesis. The study investigated the ability of DON and-for the first time of its metabolite DOM-1-to induce apoptosis, mitogen-activated protein kinase (MAPK) signalling, oxidative events and alterations of mitochondrial structure in porcine intestinal epithelial cells (IECs). The degree of DON toxicity strongly varied, depending on the cytotoxicity parameter evaluated. DON compromised viability according to the parameters of lysosomal activity, total protein content and membrane integrity, but increased viability according to assays based on mitochondrial metabolism and ATP synthesis. DON induced expression of cleaved caspase-3 (maximum induction 3.9-fold) and MAPK p38 and p42/p44 (maximum induction 2.51- and 2.30-fold, respectively). DON altered mitochondrial morphology, but did not increase intracellular ROS. DOM-1-treated IPEC-J2 remained unaffected at equimolar concentrations in all assays, thereby confirming the safety of feed additives using DON- to DOM-1-transforming bacteria. The study additionally highlights that an extensive multi-parameter analysis significantly contributes to the quality of in vitro data.