Alternariol (AOH) and alternariol-9-methyl ether (AME) are major toxins produced by fungi of the genus Alternaria. In order to simulate their in vivo intestinal absorption and metabolism, AOH and AME have been studied in differentiated Caco-2 cells and in the Caco-2 Millicell® system in vitro. AOH was found to be readily conjugated to two glucuronides and one sulfate, whereas AME gave rise to one major glucuronide and one sulfate. Whereas the glucuronides of AOH and AME were sequestered about equally well into the basolateral and the apical compartment, the sulfates of both toxins were preferentially released to the apical side. Unconjugated AOH but not AME aglycone reached the basolateral chamber. The apparent permeability coefficients (Papp values) were calculated for the aglycones as well as total mycotoxin-associated compounds using an initial apical concentration of 20 µmol/l AOH or AME. Based on these Papp values, AOH must be expected to be extensively and rapidly absorbed from the intestinal lumen in vivo and reach the portal blood both as aglycone and as glucuronide and sulfate. In contrast, intestinal absorption of AME appears to be poor and sluggish, with no AME agylcone and only AME conjugates reaching the portal blood.