The advent of new high throughput sequencing technologies has paved the way for microbiome research, opening up entirely new perspectives on the complex and diverse ecosystems of the human body. One of the main findings was that it became clear that in contrast to the widely held dogma the urinary tract is not a sterile environment. As for all niches of the human body, a well-balanced microbiome is an essential part for the physiological functioning of the urinary tract and therefore it must be considered a prerequisite for health. The dysbalance of the microbiome is now seen as having a considerable impact on the pathogenesis of a plethora of diseases. Its role in benign disorders, such as interstitial cystitis, urinary urge incontinence and chronic prostatitis/chronic pelvic pain syndrome as well as participation in malignant conditions, such as prostate cancer has recently been revealed. The contribution of the urinary microbiome to the pathogenesis and progression of lower urinary tract symptoms due to benign prostatic obstruction are currently under investigation.