In this prospective study the performance of transrectal or transvaginal endoscopic ultrasonography (EUS) was compared with that of computed tomography (CT) in the diagnosis of perirectal fistulae, abscesses and diffuse inflammatory changes in the lower pelvis in 25 patients with Crohn's disease. Results were verified by surgery in eight patients and by correlation with findings on endoscopy, barium radiography and fistulography, and the clinical course in all other patients. EUS was superior to CT in diagnosing fistulae (14 vs 4 correct diagnoses) and inflammatory infiltration of the lower pelvic muscles (11 vs 2 correct diagnoses). The methods were equivalent in diagnosing perianorectal abscesses. CT was superior in the detection of inflammatory changes in the pararectal fasciae and fatty tissue which could not be detected by EUS. It is concluded that EUS should be used as the primary method for diagnosing perianorectal changes in patients with Crohn's disease especially in the case of fistulae and abscesses, having the added advantage of lack of radiation for the patient.