We will discuss what is known concerning the role of the human urogenital microbiome in lower urinary tract physiology and the methods to assess these microbial communities in research and clinical practice. We will review data available for a few urologic conditions, such as urinary tract infection, urgency incontinence, and genitourinary pain, as well as the potential clinical and surgical implications for this emerging research. We will briefly explore how to use this knowledge in clinical practice based on the available evidence and the next steps to deepen our understanding of these key players in human urinary tract function.