Prebiotic oligosaccharides influence the intestinal microbiota and can positively modulate the infant's immune system. It was demonstrated that a special prebiotic mixture (Immunofortis (R)) of short-chain galacto-oligosaccharides (scGOS) and long-chain fructo-oligosaccharides (lcFOS) can reduce the cumulative incidence of atopic dermatitis (AD) in infants at risk for allergy as determined using the AD symptom score (SCORAD). Additionally, it was shown very recently that immunoglobulin free light-chain (Ig-fLC) might be involved in the pathophysiology of allergic disease. Increased Ig-fLC concentrations were found in patients suffering from AD, cow's milk allergy, allergic rhinitis, or asthma. In this study, the effect of supplementation of scGOS/lcFOS on the Ig-fLC plasma concentrations in infants at risk for allergy was assessed. The plasma kappa and lambda Ig-fLC concentrations were measured in a double-blind, placebo-controlled, randomized trial, in which infants at risk for developing allergic disease received a hypoallergenic whey formula containing 8 g/l of the scGOS/lcFOS mixture (n = 34) or maltodextrin as a placebo (n = 40) for 6 months. After intervention, plasma samples were collected, and total plasma concentrations of lambda and kappa Ig-fLC were analyzed using ELISA. Total kappa and lambda Ig-fLC plasma concentrations were higher in infants suffering from AD when compared to infants without any sign of AD. In infants receiving the prebiotic mixture, the Ig-fLC levels were significantly lower compared to the placebo-fed infants (p < 0.001). Interestingly, lambda Ig-fLC concentrations were positively correlated with total IgE (p < 0.05). These data demonstrate for the first time that the specific scGOS/lcFOS mixture lowered kappa and lambda Ig-fLC plasma concentrations in infants at high risk for allergies when compared to infants receiving placebo formula. Because Ig-fLC concentrations were increased in infants suffering from AD, this may have contributed, at least in part, to the reduced incidence in AD as described previously. This suggests a possible role for Ig-fLC in the pathophysiology of AD in infants at risk for allergy development.