Climatic changes are expected to introduce extreme weather events such as heavy precipitations, which might in turn contribute to the occurrence of infectious diseases. We conducted a study in Taiwan to evaluate the effects of precipitation following typhoons on the incidence of selected infectious diseases from 2006 to 2015, including acute viral hepatitis A, amoebiasis, enterovirus with severe complications, dengue fever, shigellosis, and scrub typhus. Using a governmental classification system, we stratified precipitation levels into “no precipitation,” “normal precipitation,” and “heavy precipitation.” We found that compared to no precipitation, normal precipitation was associated with increased risks of dengue fever (relative risk [RR]=1.19; 95% confidence interval [95%CI]: 1.12-1.27) and shigellosis (RR=1.59; 95% CI: 1.05-2.41). While heavy precipitation was associated with further increases in the risks, only the risk of dengue fever reached statistical significance (RR=2.15; 95%CI: 1.74-2.66). Public health practitioners should anticipate possible outbreaks of infectious diseases after typhoons.