Biopsy from the edge of a septal perforation is performed to diagnose potentially significant aetiological conditions, including malignant pathology and Wegener's granulomatosis. However, it is common for the histological result to be undiagnostic and unhelpful in planning an individual patient's management. To clarify the role of septal perforation biopsy, we reviewed all biopsies performed on our patients over a 13-year period. Of the 65 biopsies performed, in 63 patients, none had a histological result which changed the clinical diagnosis made before biopsy. Forty-three patients had clinically benign perforations biopsied, and no histology other than chronic inflammation was obtained. In 16 patients with a clinical vasculitis, none had this diagnosis confirmed histologically. One positive biopsy was obtained from two patients with clinically malignant perforations yet both were treated for T-cell lymphoma. The subsequent management of all patients was based on their clinical diagnosis rather than their biopsy results. We suggest only clinically malignant perforations are worthwhile biopsying.