The purpose of this study was to compare prospectively the diagnostic yield of anal endosonography (AES) and magnetic resonance imaging (MRI) in the assessment of perianal fistulae and abscesses. There were 39 patients (14 men, 25 women; mean age, 40 years) who underwent AES, performed with a 10-MHz rotating endoanal probe and MRI at 1.0 T (axial and coronal T2-weighted turbo spin-echo (TSE) and turbo-STIR sequences). Fistulae were classified as subcutaneous, intersphincteric, transsphincteric, high (i.e., high extrasphincteric or suprasphincteric), rectovaginal, and horseshoe and were compared with the surgical findings in all patients. Overall, 58 fistulae (subcutaneous, N = 7; intersphincteric, N = 9; transsphincteric, N = 16; high, N = 17; rectovaginal, N = 5; and horseshoe, N = 4) were detected at surgery. MRI showed a sensitivity of 84% and AES of 60% (P <.05). False-positive diagnoses were made in 6 patients (15%) with MRI and in 15 patients (26%) with AES, for a specificity of 68% and 21%, respectively (P <.05). Our findings show that MRI is superior to AES in the assessment of fistula-in-ano before major surgery. AES should be used only for orientation before minor procedures, such as incision or drainage of subcutaneous fistulae. Copyright 2001 Wiley-Liss, Inc.