Background: We designed a prospective study of diagnostic accuracy which compared pelvic MRI and 3D-EAUS versus pelvic MRI alone in the preoperative evaluation and postoperative outcomes of patients with perianal fistulas. Methods: The sample size was 72 patients and was divided into two imaging groups. MRI alone was performed in the first group. Both MRI and 3D-EAUS were performed in a parallel fashion in the second group. Surgical exploration took place after two weeks and was the standard reference. Park’s classification, presence of a concomitant abscess or a secondary tract and location of the internal opening were recorded. All patients were re-evaluated for complete fistula healing and fecal incontinence six months postoperatively. All the collected data was subjected to statistical analysis. Results: Group MRI included 36 patients with 42 fistulas. Group MRI + 3D-EAUS included 36 patients with 46 fistulas. The adjusted sensitivity and negative predictive value were 1.00 for most fistula types in the group of combined imaging. The adjusted specificity improved on intersphincteric fistulas in the same group. The adjusted balanced accuracy improved on all fistula types, except for rectovaginal. The combination of imaging methods showed improved diagnostic accuracy only on the detection of a secondary tract. Healing rate at six months was 100%. Fecal incontinence at six months didn’t present a statistically significant difference between the two groups (Fisher's exact test p-value > 0.9). Patients with complex perianal fistulas had a statistically significant higher probability to undergo a second surgery (x² test p-value=0.019). Conclusion: The combination of pelvic MRI and 3D-EAUS showed improved metrics of diagnostic accuracy and should be used in the preoperative evaluation of all patients with perianal fistulas, especially in those with complex type.