For phalloplasty, two urethral lengthening (UL) segments are required to extend the urethra from where it is to the tip of the new penis. The first UL segment is made from minora tissue and lengthens the urethra to the tip of the native penis. This is called the pars fixa, or PF, urethra. The second UL segment is created through the flap (RF or ALT) where a segment of the rectangular RF or ALT flap is rolled into the urethra; the remainder of the flap is rolled on the outside of the urethra to become the new penis (or neophallus). This segment of UL is called the pars pendulans, or PP, urethra. For metoidioplasty, UL is composed mostly of minora tissue.

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Urethral strictures and fistulas can develop after phalloplasty and metoidioplasty. Fistulas lead to leakage of urine from a hole (or holes) in the urethra. Strictures lead to narrowing of the urethra and a resultant weak urinary stream. Fistulas may heal on their own; strictures require reconstruction. Tracking a patient's urinary symptoms over time will help determine the likelihood of having a urethral problem, which is why regular followup with reconstructive urology is important. One metric used for followup is uroflowmetry. An easier at home test is to evaluate for an average flow rate. An average flow rate can be calculated by measuring urine volume (milliliters) and dividing it by time (seconds). 

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