The human microbiome is currently being studied with increasing interest. The microbiome refers to the microorganisms living in the body and their genetic information. The human body is known to contain 1.3 to 10 times more microorganisms than human cells. The Human Microbiome Project was started in 2007 to characterize the human microbiome and analyze its role in human health and diseases. Based on the recent microbiome literature, alterations in the microbiome are associated with several non-urological diseases in pediatrics, such as infantile colic, necrotizing enterocolitis, asthma, atopy, obesity, type-1 diabetes, autism, atopic dermatitis, psoriasis, and bronchial asthma. While some urinary microbiome studies (including prostate cancer, bladder cancer, interstitial cystitis, urge urinary incontinence, overactive bladder, stone disease, and urinary tract infections) have been conducted in adults, there are very few pediatric urinary microbiome studies. This study reviews the role of the urinary microbiome in urinary tract diseases from a pediatric urological perspective.