The aim of this study was to determine the occurrence of on-farm risk factors and health effects associated with contamination of dairy feeds with aflatoxins (AFs), zearalenone (ZEN), trichothecenes (T-2), deoxynivalenol (DON), and fumonisins (FB) in Jordan. A pre-tested and validated questionnaire was used to determine on-farm practices and health effects associated with high levels of mycotoxins. A total of 88 feed samples were collected from the 37 farms participating in the study and analyzed using commercially available ELISA kits. The mean total AF concentration exceeded the European Union (EU) limit in alfalfa (4%) and total mixed ration (TMR) (3%) samples. Similarly, levels exceeding EU limits were observed for T-2 in alfalfa (29%), TMR (30%), and corn silage (4%). The average concentrations of ZEN and FB were 300 ppb and 11,638 ppb, respectively, which were below the EU maximum limits in all feed samples examined. Intensive management system (OR?=?7.70), imported feed (OR?=?3.40), feed storage on the farm for more than 1-month duration (OR?=?7.90), and not using antitoxins (OR?=?2.30) were significantly (P?<?0.05) associated with high levels of mycotoxins in feed samples. A significant correlation (P?<?0.05) was evident between the presence of mycotoxins in dairy feed and feed refusal (R?=?0.70), low milk production (R?=?0.50), diarrhea problems (R?=?0.60), infertility (R?=?0.50), and repeated breeder problems (R?=?0.80). Results show that mycotoxin contamination in dairy feeds is a problem in Jordan, and appropriate measures need to be undertaken to reduce risks to human and animal health and improve production.