Confocal laser endomicroscopy (CLE) can serve as a useful adjunct imaging modality for targeted endoscopic biopsies during surveillance of Barrett's esophagus (BE). In addition, CLE may also have potential roles during therapeutic procedures that include localization of pathology, targeting of resections, guiding which therapy to use, and determining adequacy of treatment. This case series illustrates a range of cases in which endomicroscopy was performed during the procedure and offers possibilities of real-time decision-making to select specific therapies in patients with known high-grade dysplasia (HGD) and intramucosal carcinoma in the setting of BE presented for endoscopic treatment or follow-up. Patients with BE with HGD and intramucosal carcinoma presented for management for initial treatment or follow-up. Examinations were performed sequentially with detailed white light endoscopy, narrow band imaging (NBI), acetic acid, and CLE. This is a retrospective case series describing the characteristics of the exam findings and illustrating the role of endomicroscopy on real-time case management. Seven patients with Barrett-associated neoplasia underwent endomicroscopy as part of their endoscopic examination. CLE confirmed findings of neoplasia seen with red flag techniques such as NBI, and in one case independently suggested findings of neoplasia. In the majority of cases, these findings were incorporated into the decision of which modality of treatment was used. Future prospective studies should be done to validate the role of endomicroscopy in BE.