The guinea-pig is often used for experimental studies in urology. However, the anatomy of the lower urinary tract of the guinea-pig is poorly described in the literature. The structure and function of the lower urinary tract, i.e. continence, micturition and sexual function, are closely related to the gross anatomy of the pelvis and the fine structure of the musculature. We investigated the anatomy and histomorphology of the lower urinary tract by serial sections in male guinea-pigs and compared it to that in humans. Immunohistochemical stainings for alpha-smooth muscle cell actin were used to differentiate between smooth and striated muscles. By using whole pelvic preparations, including all internal organs preserved in their in situ location for three-dimensional reconstruction, we developed three-dimensional models, which elucidate the spatial relationship of all muscular structures and can help to deduce functional aspects of lower urinary tract function. In the guinea-pig, most of the muscles found in humans can be demonstrated in comparable location and extension. However, the structure of the prostate and the existence of the so-called coagulation glands define a significant difference in the morphology of the prostatic urethra.