The TARGIT-A Trial is an international randomized, prospective trial comparing intraoperative radiotherapy (IORT) for equivalence to external beam radiotherapy (EBRT) following lumpectomy for invasive breast cancer in selected low-risk patients; early results suggest that outcomes are similar. In addition to effectiveness data and cost considerations, the preferences of patients should help inform practice. This study was undertaken to explore and quantify preference in choosing between IORT and the current standard, EBRT. Eligible subjects were current or past candidates for breast-conserving surgery and radiation being seen at the University of California, San Francisco Breast Care Center. A trade-off technique varying the risk of local recurrence for IORT was used to quantify any additional accepted risk that these patients would accept to receive either treatment. Patients were first presented with a slideshow comparing EBRT with the experimental IORT option before being asked their preferences given hypothetical 10-year local recurrence risks. Patients were then given a questionnaire on demographic, social and clinical factors. Data from 81 patients were analyzed. The median additional accepted risk to have IORT was 2.3 % (−9 to 39 %), mean 3.2 %. Only 7 patients chose to accept additional risk for EBRT; 22 accepted IORT at no additional risk; and the remaining 52 chose IORT with some additional risk. Patients weigh trade-offs of risks and benefits when presented with medical treatment choices. Our results show that the majority of breast cancer patients will accept a small increment of local risk for a simpler delivery of radiation. Further studies that incorporate outcome and side effect data from the TARGIT-A trial clarify the expected consequences of a local recurrence, and include an expanded range of radiation options that could help guide clinical decision making in this area.