Background: Allergic diseases are common and represent a considerable health and economic burden worldwide. We aimed to examine the effect of a combination of two probiotic strains administered in late infancy and early childhood on the development of allergic diseases and sensitization. Methods: In this double-blind, placebo-controlled intervention trial, participants were randomized to receive a daily mixture of Lactobacillus rhamnosus and Bifidobacterium animalis subsp lactis or placebo—starting prior to attending day care. The intervention period was 6 months, and the parents answered web-based questionnaires on allergic symptoms and doctor's diagnosed allergic disease monthly. IgE was measured at baseline and follow-up. Results: A total of 290 participants were randomized: 144 in the probiotic group and 146 in the placebo group. Mean age at intervention start was 10.1 months. At follow-up (mean age 16.1 months), the incidence of eczema was 4.2% in the probiotic group and 11.5% in the placebo group (P = 0.036). The incidence of asthma and conjunctivitis did not differ between groups, and no children presented with rhinitis. Sensitization was equal in the two groups at intervention start (7.5% and 9.5%, respectively), and two children in each group were sensitized during the intervention. Conclusions: We observed a significantly lower incidence of eczema in the probiotic group compared to the placebo group. The probiotics were administered in late infancy—prior to attending day care—suggesting a broader window of opportunity using probiotics in the prevention of eczema. The incidence of asthma, rhinitis, conjunctivitis, and sensitization did not differ.