Supplementary l-tryptophan (l-Trp) limits the decrease of feed intake and growth in Enterotoxigenic Escherichia coli F4 (ETEC) susceptible pigs upon oral challenge with this pathogen. Susceptibility to ETEC is genetically controlled and related to the presence of receptors for the F4 fimbriae (F4R). We aimed to assess if dietary Trp affects genes involved in the intestinal barrier of healthy pigs carrying or not the F4R. Thirty-six littermate weaning pigs were selected to have potentially eighteen ETEC-susceptible and eighteen ETEC-non-susceptible subjects, based on a Mucin 4 gene polymorphism. For 21 days they were fed a diet with 0.17 or 0.22 ileal digestible Trp:Lys ratio. Using the test of ETEC adhesion to the intestinal villi, the pigs were divided into F4R negative (no bacteria adhering, F4R−), F4R positive (F4R+), and F4R mildly positive (F4Rm+). A preliminary test (GeneChip® Porcine Genome Array) highlighted the differentially expressed genes in the jejunum of 3 F4R− and 3 F4R+ pigs. The expression of the most interesting genes was assessed on the whole sample. In F4R+ pigs, Trp reduced the mRNA of four genes involved in the intestinal barrier and/or induced by several bacteria-associated molecular patterns, like lipopolysaccharide (LPS) (REG3G, Regenerating islet-derived 3 gamma; SFTPD, Surfactant pulmonary-associated protein D; CFB, Complement factor B; LBP, LPS-binding protein) (P