Although gut microbiota has been studied relatively extensively in the context of allergic diseases, there have been several contradictions between these studies. By applying high-throughput sequencing, we aimed to analyze the differences in gut microbiota between atopic and healthy children at 5 and 12 years of age. 51 stool samples were collected from 14 atopic and 15 healthy children and analyzed with 454 pyrosequencing of the 16S rRNA gene. At the ages of 5 and 12 years, Bacteroides, Prevotella, and Dialister dominated gut microbiota in both atopic and healthy groups of children. Children in the atopic group had lower abundance and prevalence of Akkermansia in gut microbiota than their healthy counterparts. Thus, the composition of gut microbiota does not seem to be significantly different between atopic and healthy children, but lower abundance and prevalence of Akkermansia indicate that this bacterium may accompany or play a role in IgE-mediated atopic diseases.