Introduction Breast-conserving surgery (BCS) is established as a standard treatment option for women with early-stage invasive breast cancers. Margin status predicts local disease recurrence. Up to 59 % of patients may undergo re-excision of their tumour cavity to establish clear margins. Intra-operative margin assessment may decrease re-excision rates. It is unclear if this procedure increases operative time. We compared intra-operative macroscopic assessment of margins, routine cavity shave margins and no formal intra-operative margin assessment to assess their impact on re-excision rates, residual disease burden and operative time. Methods Over a 42 month period, 188 patients from our retrospective breast cancer database were reviewed in our study. Of these, 68 had macroscopic margin assessment, 70 had cavity shave margins and 50 had no formal intra-operative assessment. Statistical analysis was performed as appropriate. Results Formal intra-operative margin assessment had a re-excision rate of 25 %, compared with 34 % for those without formal assessment. Formal assessment had a significantly reduced likelihood of having residual disease following the primary procedure (p = 0.02). Close margins ( Conclusion Directed intra-operative margin assessment reduces residual disease burden in BCS without increasing operative duration.