ABSTRACT The use of high-throughput sequencing technologies has played a major role in debunking the myth of human urine sterility. With new technologies-16S rRNA amplicon sequencing, metagenomic sequencing- several genera, phyla and species of bacteria resident in the human urinary tract have been discovered and their role in health and disease have been reported. The focus of this review includes classification of microorganisms resident within the urinary tract, techniques used to sample, identify and classify these organisms, and the impact of resident microorganisms on normal and abnormal urinary tract function.