Alterations in the composition and reduced diversity of the infant microbiome are associated with allergic disease in children. Further, an altered microbiota is linked to immune dysregulation, including skewing of different T-helper (Th)-subsets, which is also seen in atopic individuals. The aim of this study was therefore to investigate the associations between gut lactobacilli and Th-related plasma factors in allergy-development during childhood. 194 children with known allergy status at 1 year of age were followed to 10 years of age. We used real-time PCR to investigate the presence of three lactobacilli species (Lactobacillus (L) casei, L. paracasei, L. rhamnosus) in infant fecal samples (collected between 1 week and 2 months of age) from a subgroup of children. Plasma chemokines and cytokines were quantified at 6 months, and at 1, 2, 5 and 10 years of age with Luminex or ELISA. FeNO was measured and spirometry performed at 10 years of age. The data was analysed by non-parametrical testing and a logistic regression model adjusted for parental allergy. An absence of these lactobacilli and higher levels of the chemokines BCA-1/CXCL13, CCL17/TARC, MIP-3α/CCL20 and MDC/CCL22 in plasma at 6 months of age preceded allergy-development. The presence of lactobacilli associated with lower levels of atopy-related chemokines during infancy together with higher levels of IFN-γ and lower FeNO during later childhood. The results indicate that the presence of certain lactobacilli species in the infant gut may influence allergy-related parameters in the peripheral immune system, and thereby contribute to allergy-protection.This article is protected by copyright. All rights reserved.