The objective of this study was to investigate the risk factors for and prevalence of clonorchiasis in Miaoli County, Taiwan. In 2009, 6,929 subjects were randomly selected in Miaoli County and given a questionnaire to fill out regarding risk factors for clonorchiasis; the response rate was 69%. Stool sample was obtained from each participant who filled out the questionnaire and examined using the merthiolate-iodine-formaldehyde concentration (MIFC) technique to determine the presence and concentration of Clonorchis sinensis eggs. Fifty-one subjects gave a history of clonorchiasis (prevalence rate 0.7%). Seven stool samples were positive for C. sinensis (prevalence rate 0.1%). Shihtan Township (5.0%) in Miaoli County had the highest prevalence of clonorchiasis. Using logistic regression, we found people who often fished (OR: 3.65, p=0.013) or who had a family member with a history of clonorchiasis (OR: 18.7, p<0.001) were more likely to have it. We also found tourists who traveled to China and ate fish there (OR: 2.46, p=0.105) or who owned a fish pond (OR: 1.93, p=0.128) were more likely to get clonorchiasis. The prevalence of clonorchiasis in Miaoli County was relatively low, which can be explained by good sanitation and personal hygiene. The Public Health Department of Taiwan should warn Taiwanese travelers about high risk areas for contracting clonorchis infection and encourage these travelers to avoid going fishing or eating raw fish in high risk areas.