Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhoea in children in resource-limited countries and of travellers diarrhoea. The ileal proteomics change after ETEC challenge is less characterised. Here in this study changes of ileal proteins post ETEC challenge in weaned pigs are studied. In total, 5151 ileal proteins were successfully annotated and 9 proteins had significantly different abundance between the ETEC and CON pigs.