In cattle, Eimeria produces clinical disease with different degrees of severity, depending on the dominant species. Eimeria bovis triggers severe intestinal damage, while E. alabamensis causes minimal damage. Cytokines and other factors derived from epithelial cells play important roles in inflammatory and immune responses in intestinal tissue. This study aimed to obtain a detailed view of IFN-gamma and IL-4 mRNA expression as well as of activation of NF-kappaB p50 and p65 subunits induced by E. bovis or E. alabamensis in intestinal epithelial cells by means of a RT-PCR assay and a NF-kappaB p50/p65 ELISA-based kit, respectively. Our results demonstrate that infection by both Eimeria species enhances IL-4 mRNA expression in intestinal cells. However, IL-4 was expressed more intensely in cells incubated with E. bovis whereas IFN-gamma levels were higher and detected at an earlier time in cells infected with E. alabamensis. NF-kappaB was activated in infected cells irrespective of species, yet the activity of the p50 subunit was significantly higher in cells incubated with E. bovis. Our results suggest that the intensity of host-cell responses triggered by these two Eimeria species could be considered as potential determinants of pathogenicity.