Introduction: The aim of this prospective study was to determine whether breast specimen ultrasound (SUS) can reliably be used to confirm whether ultrasound (US) visible breast malignancies are excised with clear margins during breast-conserving surgery (BCS), in order to avoid a second operation and recurrence. Methods: A total of 95 consecutive participants with US visible malignancies, undergoing BCS, had the excised breast specimen transported to the radiology department intraoperatively. Breast SUS was used to confirm the presence of the lesion and measure the medial, lateral, superior and inferior margins. Margins < 10mm prompted a call to theatre to recommend an immediate cavity shave. The accuracy of the SUS technique in confirming the lesion is contained within the specimen, and the correlation of radial margins on US and histology was assessed retrospectively. Results: Breast SUS had 100% accuracy in confirming the presence of 99 lesions. 384 corresponding US and invasive carcinoma histological margins were compared. A 10mm or greater margin on US has a sensitivity of 56% (95% CI 21–86), specificity of 93% (95% CI 90–95) and accuracy of 92% (95% CI 89–95) in predicting no ink on tumour histologically, with a positive predictive value of 16% (95% CI 5–34) and negative predictive value of 99% (95% CI 97–99%). The area under the curve was 0.746 (95% CI 0.572–0.921). Conclusions: Breast SUS is a fast and reliable technique. Mammographically occult breast malignancies that are sonographically evident should undergo SUS to confirm the presence of the lesion and assess its macroscopic margins to avoid a re-excision.