The intermediate (membranous) part of the urethra begins at the apex of the prostate and traverses the deep perineal pouch, surrounded by the external urethral sphincter. It then penetrates the perineal membrane, ending as the urethra enters the bulb of the penis. Posterolateral to this part of the urethra are the small bulbo-urethral glands and their slender ducts, which open into the proximal part of the spongy urethra.

The spongy urethra begins at the distal end of the intermediate part of the urethra and ends at the male external urethral orifice, which is slightly narrower than any of the other parts of the urethra. The lumen of the spongy urethra is approximately 5 mm in diameter; however, it is expanded in the bulb of the penis to form the intrabulbar fossa, and in the glans penis to form the navicular fossa. On each side, the slender ducts of the bulbo-urethral glands open into the proximal part of the spongy urethra; the orifices of these ducts are extremely small. There are also many minute openings of the ducts of mucus-secreting urethral glands into the spongy urethra.

The arterial supply of distal male urethra (intermediate and spongy parts of the urethra) is from branches of the dorsal artery of the penis.

Veins accompany the arteries and have similar names.

Lymphatic vessels from the intermediate part of the urethra drain mainly into the internal iliac lymph nodes, whereas most vessels from the spongy urethra pass to the deep inguinal lymph nodes, but some lymph passes to the external iliac nodes.

The innervation of the intermediate part of the urethra is the same as that of the prostatic part: autonomic (efferent) innervation via the prostatic nerve plexus, arising from the inferior hypogastric plexus. The sympathetic innervation is from the lumbar spinal cord levels via the lumbar splanchnic nerves, and the parasympathetic innervation is from the sacral levels via the pelvic splanchnic nerves. The visceral afferent fibers follow the parasympathetic fibers retrogradely to sacral spinal sensory ganglia. The dorsal nerve of the penis, a branch of the pudendal nerve, provides somatic innervation of the spongy part of the urethra.