Background: We previously reported that a Lactobacillus acidophilus probiotic strain (LAFTI((R)) L10/LAVRI-A1) given for the first 6 months of life increased the risk of allergen sensitization at 1 year of age.Methods: To assess the effects on subsequent allergic outcomes, 153 children from the initial prevention cohort (n = 178) were reviewed at 2.5 years of age. Clinical outcomes were assessed in relation to (i) probiotic supplementation; and (ii) immune function previously assessed at 6 months of age.Results: Supplementation with this probiotic did not reduce the risk of dermatitis at 2.5 years (31/74, 42%) compared with that in placebo group (25/76, 34%). There was no significant reduction in any other allergic disease or allergen sensitization. Inhalant sensitization at 2.5 years (n = 29) was associated with higher proportions of circulating CD4+ CD25+ regulatory T-cell populations (P = 0.005) and higher allergen-induced FOXP3 levels (P = 0.003) at 6 months. This was also seen in children with dermatitis. Children with dermatitis at 2.5 years also had significantly lower toll-like receptor 4 lipopolysaccharide responses at 6 months of age (IL-12 P = 0.04, IL-6 P = 0.039) and lower polyclonal (PHA) responses (IFN-gamma P = 0.005, IL-10 P = 0.001, and IL-6 P = 0.001). Children who had previously received the probiotic had fewer gastrointestinal infections in the preceding 18 months (P = 0.023).Conclusion: The LAFTI((R)) L10 probiotic strain did not have any significant effect on allergy outcomes. Allergic children showed a number of early differences in immune function including altered regulatory T-cell markers and innate immune function.