Background. Intraoperative decision of the level of distal resection in rectal cancer is often imprecise, based exclusively on digital examination and pretherapeutic imaging. Design. Prospective, single institution, nonrandomized trial (ClinicalTrial.gov identification no. NCT01887509) to evaluate the contribution of probe-based confocal laser endomicroscopy (pCLE) to establish the optimal resection margin of rectal adenocarcinoma. The primary outcome was the concordance in the identification of lower tumor margins between pCLE and histopathology. For each patient, pCLE examination was performed on nonneoplastic and neoplastic aspects of the distal tumor margin, before and after neoadjuvant chemoradiation, or preceding surgery, if chemoradiation was not required. Biopsies were taken at the same locations. The intraclass correlation coefficient was determined. Results. Twenty-one patients were enrolled. Thirteen patients completed the full study. Six patients completed imaging only before chemoradiation. Two patients retracted their consent after inclusion. A total of 134 videos and corresponding histopathology samplings were analyzed. The sensitivity and specificity of in vivo pCLE interpretation were 0.915 (95% confidence interval [CI] = 0.840-0.970) and 0.736 (95% CI = 0.657-0.821), respectively. The sensitivity and specificity of the blinded pCLE reinterpretation were 0.930 (95% CI = 0.858-0.980) and 0.688 (95% CI = 0.600-0.770), respectively. No deep layer tumor infiltration was encountered in the samplings with superficial healthy layers. The intraclass correlation coefficient for in vivo pCLE interpretation and blinded pCLE reinterpretation were 0.747 (95% CI = 0.257-0.993) and 0.766 (95% CI = 0.280-0.995), respectively. Conclusions. This supports the concordance between pCLE and histopathology in identifying the “tumor-free” limit of a rectal tumor preceding resection.