Intraoperative consultation is frequently used during the surgical treatment of lung tumors for the diagnosis of malignancy and the assessment of surgical margins. The latter is often problematic given the nature of applied staple lines, which cannot be readily examined in frozen sections. Seventy-nine samples of surgical margins (71 staple lines and 8 open margins) from 52 lung specimens were examined using an ex vivo fluorescence confocal microscope (FCM). The diagnoses of the FCM scans were compared with the corresponding paraffin section images of the same material. The procedure provided intraoperative FCM imaging of the surgical margins and staple lines without having to remove the metal clips. Tumor-involved open margins (5/5) and tumor-involved staple lines (3/4) were correctly identified in the FCM images. The results also provided additional information to the conventional frozen sections (FS). To our knowledge, this is the first time staple lines of lung specimens have been visualized as preserved tissue using FCM. The method potentially provides an additional approach for intraoperative decisions when the margins in conventional frozen sections are unclear. Our promising results, however, need to be validated on a larger number of cases.