Abstract Background This was a prospective study designed to determine the therapeutic impact of magnetic resonance imaging (MRI) in primary fistula in ano, and to assess its effect on outcome. Methods Thirty patients with suspected primary fistula in ano underwent preoperative MRI, and the findings were revealed during surgery following examination under anaesthesia (EUA). Any effect on operative approach was noted. Outcome was assessed at a median of 12 months. Results Two patients had sinuses, one had no sepsis and 27 had fistulas: five superficial, seven intersphincteric, 14 trans-sphincteric and one suprasphincteric. MRI and EUA agreed in 15 patients and MRI findings altered the surgical approach in a further three (10 per cent); two of the latter patients were believed to have a sinus at EUA, which MRI correctly identified as a fistula, allowing definitive treatment. The therapeutic impact of MRI was therefore 10 per cent. Persisting disagreement between MRI and EUA in 12 patients mostly related to minor discrepancies in classification. Only one patient required further unplanned surgery, which was for skin-bridging rather than any new sepsis. Conclusion In experienced hands, MRI has a therapeutic impact of 10 per cent for primary fistula in ano, precipitating surgery that is likely to reduce recurrence in a small, but important, proportion of patients.