Allergic diseases including asthma, rhinitis, and food allergies affect an ever-increasing number of patients particularly in industrialized countries. Despite a role for genetic susceptibility in the development of allergies, environmental factors are increasingly recognized as being central to allergy pathogenesis. In particular, a lifestyle characterized by high hygiene standards, an excessive use of antibiotics, and the consumption of highly processed foods has been associated with a high incidence of allergic diseases. This association has led to the postulation of the ‘hygiene hypothesis,’ stating that our immune system needs to be educated by microbes to induce tolerance to harmless and self-antigens, while retaining responsiveness to pathogens. In recent years, studies using animal models of allergy have provided direct evidence that the microbiome provides protection against allergic responses. However, our understanding of the mechanisms underlying this immune-modulatory role of the microbiome in allergy is still very limited. Ongoing research efforts are beginning to uncover microbial species, metabolites, and signaling pathways instrumental in the protection against allergy. The translation of these results into human disease settings and their use for the development of future therapeutics are important goals of current allergy and microbiome research. However, already today, we can appreciate that the delicate crosstalk between our immune system and our microbiome warrants a careful reevaluation of our lifestyle particularly with regard to our diet, time spent outdoors, as well as the use of antibiotics. This article will summarize the most important and recent insights into the relationship between the microbiome and allergy