The European Food Safety Authority (EFSA) has indicated that stimulation of protective antibody titers from vaccination could be used to substantiate a supplement or food health claim on the function of the immune system related to defense against pathogens in healthy individuals. Vaccination allows exposure of the immune system to controlled quantities of antigen and also for assessment of median antibody responses and percentage of responders/non-responders, which provides indication of an integrated immune response to challenge. Probiotic vaccination studies have shown enhanced antibody titers, lower percentages of non-seroconverters and greater percentages reaching minimum cut-off titer values in healthy adults, elderly and children. These results indicate that probiotics are a good candidate to stimulate responses to vaccines and thus, according to EFSA, enhance the function of the immune system related to defense against infection. However, animal research has recently indicated that Foxp3+ T-regulatory cells, recognized suppressors of immune activity, were paradoxically associated with reduced respiratory viral morbidity without compromising viral clearance. These effects conflict with vaccine research findings, which suggest a depletion of Foxp3+ T-regs enhances the immune response. Many probiotics exert anti-inflammatory influence on the immune system and induce T-regs. Given this, caution regarding the applicability of the vaccination model as indicated by EFSA must be exercised. Induction of T-cell immune modulatory pathways may also explain the reduced duration of respiratory illness observed in probiotic clinical studies.