The aim of the present study was to test the effect of Enterococcus faecium NCIMB 10415 (E. faecium) on CD4+ T helper immune cell subpopulations and CD25+ cells in ileal lymphatic tissue after challenge with Salmonella (S.) Typhimurium DT 104. German Landrace piglets treated with E. faecium (n = 16) as a feed additive and untreated controls (n = 16) were challenged with S. Typhimurium 10 days after weaning. The expression of lineage specific T helper cell subtype master transcription factors on mRNA level was measured in the whole tissue of the gut associated lymphoid tissues (ileocecal mesenteric lymph node, ileum with Peyer’s patches and papilla ilealis) and in magnetically sorted T helper cells from blood and ileocecal mesenteric lymph nodes at two and 28 days post infection. CD25 protein expression of T helper cells was studied by flow cytometry in ileal Peyer’s patches, lymph nodes and blood. Distribution and morphology of CD25+ cells was demonstrated in situ by immunohistochemistry in paraffin embedded specimens of the ileum and the ileocecal mesenteric lymph nodes. The data provide evidence for a higher T helper 2 cell driven immune response in the control group compared to the E. faecium treated group (P < 0.05) in CD4+ magnetically sorted lymphocytes from the ileocecal mesenteric lymph nodes at two and 28 days post infection. We did not observe differences for CD25+ cells in immunohistochemistry and flow cytometry between E. faecium fed pigs and the control group, but provided a detailed description of the occurrence and morphology of these cells in the gut associate lymphoid tissues of piglets. In conclusion we suggest that (i) prolonged feeding with E. faecium can result in changes of the T helper cell response leading to a stronger infection with S. Typhimurium and (ii) that it is important to examine purified immune cells to be able to detect effects on T helper cell subpopulations.