Several studies have identified bacteria and other microbes in the bladder and lower urinary tract in the absence of infection. In women, the urinary microbiome has been associated with lower urinary tract symptoms (LUTS), however, similar studies have not been undertaken in large cohorts of men. Here we examine the urinary microbiome and its association with LUTS in a subset of 500 men aged 65 to 90 years from the Osteoporotic Fractures in Men (MrOS) study. We identified significant associations between benign prostatic hyperplasia (BPH), age, and body mass index (BMI) with several diversity metrics. Our analysis revealed complex relationships between BMI, BPH, LUTS, and alpha diversity which give insight into the intricate dynamics of the urinary microbiome. By beginning to uncover the interrelationships of BPH, BMI, LUTS, and the urinary microbiome, these results can inform future study design to better understand the heterogeneity of the male urinary microbiome.