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Background The endocytoscopy system (ECS) is a new method to provide real-time super-magnifying microscopic imaging in vivo. Routine diagnosis of amebic colitis requires multiple tests that are both time consuming and costly. Objective To determine the feasibility of ECS to directly detect the amebic parasites in vivo. Design Prospective, single-center, pilot study. Setting Tertiary-care university hospital. Patients This study involved 5 patients who were suspected to have amebic colitis by conventional colonoscopy in our institute. Interventions A super-magnifying ECS with 450 × magnification. Main Outcome Measurements We compared ECS findings with those of conventional methods—serum antibody tests and histology of colon biopsy specimens. Results We successfully visualized the amebic trophozoites in all 5 cases. In contrast, 3 specimens had positive results on serology, and 3 had positive histology results on hematoxylin and eosin staining. Limitations Pilot study with a limited number of patients. Findings were compared only with serology and histology findings. Conclusions ECS would be a useful tool for the prompt diagnosis of amebic colitis via the real-time in vivo visualization of amebic trophozoites.