Probiotics are considered to have beneficial effects on the immune system. An association between the composition of microflora and allergies has been demonstrated and modulation of microflora of infants by probiotics might reduce the risk of allergies. To investigate immune effects of probiotics administered early after birth two animal models were used: a mouse model for respiratory allergy; a rat model for experimental autoimmune encephalomyelitis (EAE). Administration of the probiotic Lactobacillus casei Shirota (LcS) started during lactation and allergy or autoimmunity were induced at an adult age. Results were compared with similar studies in rats and mice that were exposed from an adult age. Early administration of LcS significantly increased lymphocytes in the lungs of female mice and eosinophils in the lungs of male mice. LcS had no effects on ovalbumin-specific serum IgE levels and on ovalbumin-specific cytokine production by spleen cells. In adult mice, LcS enhanced ovalbumin-specific cytokine production by the spleen, whereas other parameters were not affected. Early administration of LcS to rats significantly increased the duration of clinical symptoms of EAE. This was also demonstrated previously in adult rats exposed to LcS. Timing of administration of LcS induced divergent effects on respiratory allergy and only early administration of LcS exacerbated lung inflammation. In the EAE model, LcS stimulated autoimmunity independent of the timing of administration. Our data show that immune effects of probiotics do not necessarily induce beneficial effects. It is therefore important that, in the evaluation of probiotics, efficacy and safety should be demonstrated.