With early detection, breast conservation surgery with adequate surgical margins is the standard of care. The aim of this study was to evaluate the use of pre-operative duct endoscopy (DE) to target surgical resection, improve adequate margins and reduce re-excision operations. Women with DCIS, stage I and II breast cancer suitable for breast conservation were randomized to DE-assisted wide local excision versus standard wide local excision (without DE). The primary endpoint was margin re-excision rates between the two groups. Secondary end points were: (i) volume differences of the surgical specimen; (ii) whether an extensive in situ component (EIC) influenced successful DE-guided resection. 78 women were randomized: 44 patients to no-DE and 34 patients to the DE group. The median age was 59 (49-65) and 56 (48-64) years in the two groups respectively with mean follow-up of 9.1 (4.2-11.1) years. There were 23 positive findings in 17 women in 30 successful DE procedures (17/30 = 56.7%). The surgical specimen volume, no-DE (17 [IQR 10-29] cm3) and DE 20 [IQR 12-28] cm3), did not differ, p = 0.377. The overall re-excision rate was 20/78 (26%), 9 (20%) and 11 (32% in the no-DE and DE groups, respectively, p = 0.233. This randomized clinical trial was limited by incomplete accrual. DE did not contribute to improved margin excision rates whether a target lesion was visualized or not. The presence of EIC did not improve efficacy of DE.