Background Basal cell carcinomas (BCCs) excised leaving positive tumour margins, are at a higher risk of recurrence. Accordingly, complete tumour removal with preservation of healthy tissue, aiming for low recurrence rates, is the main goal in treating BCCs. Objective The present study aimed to identify the reliability of the Whole Specimen Intraoperative Frozen Section Analysis (WIFSA) technique by comparing intraoperative WIFSA and postoperative Formalin-Fixed Paraffin-Embedded section analysis (FFPE) results in 1082 basal cell carcinomas and by assessing the recurrence rates during a follow-up period up to 10 years. Methods A single-centre retrospective cohort of all patients with BCC of the face receiving surgical excision with the WIFSA method between January 2007 and December 2013 was evaluated. We compared the intraoperative frozen section results with postoperative FFPE in order to assess accuracy of the WIFSA. Recurrence rates were assessed among all BCCs with a tumour-free margin at final excision that had a minimum follow-up of 6 months. Results A total of 996 patients with 1082 BCCs were treated with the WIFSA. Overall agreement of WIFSA with conventional postoperative FFPE was 98·8%, sensitivity and specificity being 99·0% and 98·7% respectively. We excluded 23 BCCs that still had positive tumour margins at the end of the procedure and another 67 for the analysis of recurrence rate because follow-up was shorter than 6 months. A total of 992 BCCs with a tumour-free margin at final excision had a mean follow-up of 5·6 years (mean 67 ± 27·7 months (range 6–117 months)). The total recurrence rate was 2·1% (21 out of 992 BCCs). The recurrence rate among the primary tumours was 1·6% (13 out of 828 cases) and 4·9% among the recurring tumours (8 out of 164 cases). Conclusion This study indicates that, in patients with primary or recurring BCCs, WIFSA provides a high accuracy for intraoperative specimen analysis and has a low recurrence rate after a mean follow-up of 5·6 years. Funding This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.