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This paper examines the cholera epidemics in Japan and liberated Korea south of 38th degree of latitude; epidemics which appeared to spread from repatriation ships in the spring of 1946. In particular, the paper focuses on how the General Headquarters/Supreme Commander for the Allied Powers (GHQ/SCAP) and Japanese society perceived and handled the situation in which many cholera patients and carriers of cholera bacilli were found among Korean illegal entrants to Japan. At that time, cholera was prevalent in various parts of Asia, which was a disaster facilitated by the repatriation of several millions of Japanese and Japan’s former imperial subjects after the Second World War. First, the paper describes the nature of the repatriation programme including quarantine which was supervised by the US military. Then it examines the reason why illegal shipping developed between liberated Korea and post-war Japan. Finally, the paper will demonstrate how the US military and Japan viewed, imagined and represented Korea and Koreans in connection with infectious diseases such as cholera. This discursive representation was a form of “epidemiological orientalism” which embodied many imperialistic narratives about the oriental origins of diseases such as cholera. Apart from preventing disease, sanitary screening during the process of repatriation was intended to erase Japan’s imperial past and contribute to the rebuilding of Japan as a nation-state under a US-led geopolitical order in East Asia.