Endocytoscopy allows the real-time microscopic observation of living cells. Unlike the cross-sectional images obtained by conventional histology, endocytoscopy provides cellular images in a plane parallel to the surface of the mucosa. However, there is little knowledge about the endocytoscopic diagnosis of carcinomas. Using a specimen obtained by the endoscopic submucosal dissection of an intraepithelial esophageal squamous cell carcinoma, a detailed comparison between endocytoscopic and horizontal histological images was made, revealing the similarity between the images. Sharp lateral borders between atypical and normal epithelium and differences in cellularity and the sizes and shapes of the nuclei were clearly identified by endocytoscopy. Further horizontal histological investigations of this case also showed the variety of endocytoscopic images in non-cancerous and cancerous epithelia.