Magnification endoscopy enables in vivo evaluation of gastrointestinal mucosa. Furthermore, endocytoscopy (ECS) with ultra-high magnification enables in vivo observation of cellular atypia during routine endoscopic examination. The purpose of this study is to clarify the efficacy of ECS and endocytoscopic atypia (ECA) classification in various types of benign and malignant pathology in the esophagus. Consecutive 110 patients, who underwent ECS in our institution from March 2003 to December 2009, were included in this study. One hundred and forty-six esophageal lesions were classified according to ECA classification, and these endocytoscopic images were compared with histological images. We categorized endocytoscopic images into five categories according to size and uniformity of nuclei, number of cells and regularity of cellular arrangement. Eighty-one out of 89 ECA-1 to ECA-3 lesions (91.0%) corresponded to Vienna categories 1 to 3. Seventy-one out of 84 ECA-4 or ECA-5 lesions (91.2%) corresponded to Vienna category 4 or 5. Overall accuracy of ECS was 91.3%, providing images similar to conventional hematoxylin and eosin staining. In addition, with ECS, we can take an 'optical biopsy' even in patients with cardiovascular disease without interrupting anticoagulant therapy. A newly designed single charge-coupled device endocytoscope allows observation of target tissue noninvasibly from regular magnification to ultra-high magnification. The development of ECS has opened the door to in vivo cellular imaging, enabling endoscopic diagnosis of tissue cytological atypia during routine endoscopic examination.