The hygiene hypothesis suggests that the increased prevalence of allergic diseases has resulted from a relative lack of microbial stimuli during infancy and early childhood. Children with atopic diseases have different commensal bacterial groups in the gut compared to non-atopic children, and differences are also found between countries with high and low incidence of atopic diseases. Probiotics are defined as live microorganisms that provide benefits to the health of a host by altering the host's microflora when they are administered in adequate amounts. They are being investigated for possible roles in managing allergic diseases. To date, the evidence that probiotics can be used to treat or prevent allergic diseases of children remains controversial. We reviewed recent randomized, double-blinded, placebo-controlled clinical trials using probiotics for allergic diseases of children and evaluated their clinical efficacy, possible mechanisms, dosage, and safety for managing allergic diseases of children. The current data are insufficient to strongly recommend probiotics as a standard treatment or preventative measure for pediatric allergic disease. More studies are needed to standardize study designs, bacterial strains, dosages, and durations for different allergic diseases of children.