Porcine oedema disease is caused by Escherichia coli serotypes that produce potent Shiga toxins. Our aim was to compare the pathogenic potential of porcine and human Shiga toxin-producing E. coli (STEC) isolates harbouring the same panel of clinically important virulence genes in a Caco-2 epithelial cell culture system. The response of Caco-2 cells to STEC infection was investigated by trans-epithelial-electrical-resistance and microarray analysis. Porcine isolates induced a greater reduction in barrier function at 4hours compared to human isolates. A total of 44 genes were differentially expressed in Caco-2 cells exposed to porcine and human isolates. We concluded that while porcine STEC strains had the potential to affect human epithelial cells, they demonstrated host specific mechanisms of virulence that were different to the human isolates.