The morphoeic (or sclerosing) basal cell carcinoma (mBCC) is the most aggressive subtype, as it spreads into the dermis beyond the clinically visible or palpable borders, making complete excision difficult. Our aim was to identify variables in the surgical management that might increase the rate of complete resection, so we made a retrospective study of 97 mBCCs. One-stage procedures (frozen section analysis) had a higher rate of complete resection (63 of 69, 91%) than two-stage procedures (permanent section analysis) (19 of 28, 68%, p<0.05). The false negative rate of frozen section analysis was 9%. Experienced surgeons had more complete excisions and a lower rate of operative re-excisions. The use of frozen section analysis is an effective way of judging invasion of margins by mBCC. The estimation of tumour margins and the treatment of mBCC requires substantial clinical experience.