The so-called hygiene hypothesis is, at least in part, accountable for the increase in allergic diseases in the developed countries. Although there is support for one of its primary predictions that host-microbe interactions in early life have longterm effects on the development of disease across populations, the theory has already proven to be imperfect as many more recent increases in certain diseases cannot be explained by the hygiene hypothesis. Nevertheless, many research groups are interested in the host-microbe interactions and are exploring the use of "live micro-organisms which, when administered in adequate amounts, confer a health benefit to the host" (probiotics) and "selectively fermented ingredients that result in specific changes, in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health" (prebiotics) to reduce the allergic disease onset or clinical outcomes. As the definitions of pre- and probiotics by itself were already adapted after their original dictation, it is not surprising that producing generalistic conclusions on the effectiveness of pre-, pro and synbiotic intervention in allergic diseases is very challenging as large differences exist in used species, methodologies, prebiotic(s) (mixtures) and probiotic strains. In this review we elucidate on the hurdles in describing prebiotics, probiotics and the combination being synbiotics in allergic manifestations.