Allergic diseases including allergic rhinitis and asthma are increasing in the developing world, related to a westernizing lifestyle, while the prevalence is stable and decreasing in the industrialized world. This paper aims to answer the question if prevention and/or treatment of allergic rhinitis and asthma can be achieved by administrating pro-, pre- and/or synbiotics that might contribute to stabilizing the disturbed microbiome that influences the immune system through the gut–lung axis. We searched for relevant English articles in PubMed and Google Scholar. Articles interesting for the topic were selected using subject heading and key words. Interesting references in included articles were also considered. While there is substantial evidence from animal studies in well controlled conditions that selected probiotic strains may offer benefits in the prevention of wheezing and asthma, outcomes from clinical studies in infants (including as well pre- and postnatal administration) are disappointing. The latter may be related to the multiple confounding factors such as environment, strain selection and dosage, moment of administration and genetic background. There is little evidence to recommend administration of pro, pre- or synbiotics in the prevention of asthma and allergic rhinitis in children.