The available E. coli vaccines involve two main types (inactivated and live non-pathogenic) and two routes of administration (oral and parenteral) but the mechanism by which both vaccines and routes of administration work is not yet fully elucidated. The influence of a parenteral vaccine (PV) and an oral one (OV) was studied by analyzing the gene expression of biomarkers indicating cellular infiltration (calprotectin, CAL), tight junction proteins (occludin OCL, and zonulin ZON) that maintain intestinal paracellular integration and two proinflammatory (IFN-γ) and anti-inflammatory (TGF-β) mediator cytokines, as well as histomorphology and IgA production cell density. Differences were observed in CAL, more infiltrated in orally vaccinated animals; OCL also increased in orally vaccinated animals, and higher density of IgA-producing cells in ileum for orally vaccinated groups. Cytokine expression is also different; and there is a lower mRNA for IFN-γ in the parenteral than in the oral vaccinated animals. Finally, the villus height-to-crypt depth ratio was higher in the orally vaccinated groups. The data collectively show clear and different effects derived from the use of each type of vaccine, route of administration and regimen. The results suggest a more rapid and direct effect of oral vaccination and a state of suppression in the absence of a second oral stimulus by the pathogen.