Atopic Dermatitis (AD) has an increasing incidence and the real cause of the disease is not known yet. Probiotics may be involved in AD prevention, but their role is controversial. The purpose of our study was to evaluate the role of probiotics in AD occurrence. We carried out an extensive search on this topic in the international databases (Pubmed, Scopus,Web of knowledge, EBSCO, ARTO, Google Scholar, ClinicalTrials.gov.) selecting only those studies where the role of probiotics in AD occurrence was analysed. For the selected studies we calculated odds ratio (OR) and 95% confidence interval (CIs). Initially, we found 1513 articles, of which only 26 studies fulfilled our criteria. After exclusion of studies on the same populations, 16 studies were included in the final analysis. The meta-analysis of these studies revealed that probiotics administration confers protection against AD occurrence (OR = 0.64, P < 0.001). The subgroup meta-analysis, in general population and population at high risk for allergies, suggested that probiotics administration is protective for AD development in both subgroups (OR = 0.53, P = 0.005; OR = 0.66, P < 0.001). Additional subgroup analysis showed that probiotics prenatal administration followed by postnatal administration was protective (OR = 0.61, P < 0.001) unlike only administration in postnatal period (OR = 0.95, P < 0.82). Finally, the subgroup analysis based on the type of treatment suggested that both Lactobacillus alone and Lactobacillus with Bifidobacterium are protective against AD (OR = 0.70, P = 0.004; OR = 0.62, P < 0.001). Probiotics seem to have a protective role in AD prevention if there are administration in pre and postnatal period in both general and allergic risk population.