Colonization of germ-free (GF) mice has been shown to induce the gastrointestinal form of the selenium-dependent glutathione peroxidases, GPx2. Since bacterial colonization of the gastrointestinal tract is associated with stress, we aimed to clarify how bacteria affect selenoprotein expression in unstressed conditions. GF and conventional (CV) FVB/NHan(TMHsd) mice were fed a selenium-poor (0.086 ppm) or a selenium-adequate (0.15 ppm) diet for 5 weeks starting from weaning. Each group consisted of five animals. Specific glutathione peroxidase (GPx) and thioredoxin reductase (TrxR) expression was measured in plasma, liver and intestinal sections by activity, protein and mRNA level as appropriate. Under selenium-adequate conditions, selenoprotein expression did not differ in GF and CV mice. Under selenium-limiting conditions, however, GF mice generally contained higher GPx and TrxR activities in the intestine and liver, higher GPx1 protein and RNA levels in the liver, higher GPx2 protein levels in the proximal and distal jejunum and colon and higher GPx1 and GPx2 RNA levels in the colon. In addition, higher selenium concentrations were estimated in plasma, liver and cecum. All differences were significant. It is concluded that bacteria may compete with the host for selenium when availability becomes limiting. A variable association with different microorganisms might influence the daily requirement of mice for selenium. Whether the microbiota also affects the human selenoprotein status appears worthy of investigation.