Saccharomyces boulardii (S. boulardii) is a probiotic and used in the prevention or treatment of diarrhoea. Saccharomyces boulardii has many mechanisms to protect the host against diarrhoeal pathogens. It might modulate the immune system. In this study, the influence of S. boulardii on the secretion of cytokines from intraepithelial lymphocytes (IELs) infected with Escherichia coli (E. coli) and Candida albicans (C. albicans) was investigated in vitro. Cytokine levels were determined by enzyme-linked immunosorbent assay. The secretion of proinflammatory cytokines such as interleukin (IL)-1beta was decreased in the infected IELs incubated with S. boulardii, but different from it, anti-inflammatory cytokine levels such as IL-4 and IL-10, however, were found to be higher. These findings demonstrated that S. boulardii may have protective effects against diarrhoeal pathogens by reducing the proinflammatory response.