Associations between antimicrobial use and risk of enteric infection with intestinal protozoa are scarcely studied. The aim of this study was to quantify the risk of Dientamoeba fragilis infection conferred by exposure to antimicrobials. We conducted a registry-based retrospective cohort study of 9,945 Danish patients investigated for D. fragilis infection between 2008 and 2011, using data from the Danish Register of Medicinal Product Statistics, and calculating relative risks (RR) for D. fragilis infection by stratified binary regression. Furthermore, we conducted a population based case-control study using controls sampled from the Danish Civil Registration System, calculating hazard ratios (HR) for D. fragilis infection by conditional logistic regression. Exposure to metronidazole was found to confer decreased risk of D. fragilis infection; however, similar associations were found for antimicrobials not commonly used to treat D. fragilis, such as broad-spectrum penicillin, fluoroquinolones, and macrolides. In contrast, mebendazole exposure was associated with increased risk. The intake of antimicrobials influences the risk of D. fragilis.