OBJECTIVE To compare transvaginal and transrectal three-dimensional ultrasound in determining the morphology and measurements of the female urethra. METHODS Sixty-five women who had not had surgery for incontinence or pelvic floor descent had transvaginal and transrectal sonography using a 7.5-MHz mechanical sector endoprobe with three-dimensional facilities. The multiplanar display of the scanned volumes allowed detailed morphologic assessment of the urethra and the measurement of distances and volumes. Statistical endpoints were: sagittal urethral diameter, maximum rhabdosphincter length and thickness, maximum thickness of the smooth muscle complex, and the volumes of the rhabdosphincter and the smooth muscle complex. Values were compared between the two approaches using Student's t-test and Bland-Altman analysis. RESULTS Both vaginal and rectal scans were feasible. However, significant differences between the two approaches were found for the sagittal diameter of the urethra (8.4 +/- 1.9 mm on vaginal vs. 11.5 +/- 2.2 mm on rectal scans, P < 0.01) and the transverse diameter of the urethra's smooth muscle complex (11.2 +/- 0.3 mm on vaginal vs. 8.6 +/- 0.2 mm on rectal scans, P < 0.001). No other variables showed significant differences. Compression of the urethra and displacement under the symphysis pubis were observed when the ultrasound probe was applied vaginally. Bland-Altman analysis showed acceptable variability for differences of distances but considerable variability for the differences of volumes. CONCLUSIONS The female urethra can be examined both vaginally and rectally by three-dimensional ultrasound. A transvaginally applied probe seems to have a compression effect on the urethra.