<b><i>Background:</i></b> Microbiota and human allergic airway diseases have been proven to be interrelated. Bacteria-derived extracellular vesicle (EV)s are known to play important roles in interbacterial and human-bacteria communications, but their relationship with allergies has not been examined yet. Urine EVs were investigated to determine whether they could be used as biomarkers for monitoring allergic airway diseases in children. <b><i>Methods:</i></b> Subjects were 4 groups of chronic rhinitis (CR), allergic rhinitis (AR), atopic asthma (AS) and healthy controls. Single voided urine samples were collected. Urine EVs were isolated and their DNA was extracted for 16S-rDNA pyrosequencing. <b><i>Results:</i></b> A total of 118 children participated in this study; 27, 39, 19, and 33 were in the CR, AR, AS, and control group, respectively. The AR had a significantly high Chao-1 index than that of controls. Principal component analysis revealed dysbiosis in the CR, AR, and AS compared to the controls. One phylum and 19 families and genera were significantly enriched or depleted in the disease groups compared to the controls; the Actinobacteria phylum and the Sphingomonadaceae family were more abundant in the AS and CR, the Comamonadaceae family, the Propionibacteraceae family, <i>Propionibacterium</i> and <i>Enhydrobacter</i> were more enriched in the CR, and the Methylobacteriaceae family and <i>Methylobacterium</i> were more abundant in each disease group, while the Enterobacteriaceae family was depleted in each disease group. <b><i>Conclusions:</i></b> CR, AR, and AS had a distinct composition of urine EVs. Urine EVs could be an indicator for assessing allergic airway diseases in children.