This essay highlights the ways in which epidemics shaped Japanese military campaigns in Taiwan in 1874 and again in 1895, as well as subsequent colonial policy after 1895. I have focused on these particular campaigns because a vast body of source materials exists which allows us not only to understand the diseases which ravaged the Japanese forces, but also to determine their effects on particular battles and subsequent Japanese military, foreign and colonial policy. For example, during the 1874 campaign in the southern tip of Taiwan, of the approximately 5,990 men at risk, only 4 soldiers were killed in battle, while 20 succumbed to battle wounds and other injuries. In contrast, 547 men died of disease, particularly malaria. During the 1895 campaign, the Japanese force of just over 50,000 men suffered horrific losses due to epidemics, with 4,642 soldiers dying of diseses as opposed to 164 killed in battle and 515 wounded or injured. Although the Japanese quickly won the war against the resistance forces, their battle against Taiwan's epidemics had only just begun, as thousands of Japanese soldiers and civilians perished during the first ears of the Japanese Occupation era (1895-1945). The Japanese soon realized that they would have to solve Taiwan's public health problems if they were to have any hope of effectively governing their new colony. As a result some of the first regulations of the colonial government concerned sanitation and quarantine measures. All in all, Japanese colonial policy and its colonial modernization of Taiwan appear to have been significantly shaped by fear of the island's epidemics and the need to bring them under control.