Besnoitia besnoiti is an apicomplexan parasite and the causative agent of bovine besnoitiosis which is considered as a re-emergent disease in Europe. A cross-sectional serological study was conducted to determine the seroprevalence and to identify risk factors associated with B. besnoiti infection in 68 dairy herds (n = 806 cows) in Jordan during the period from January to June 2007 and the spring of 2014. Data regarding herd's management was obtained by filling questionnaires through personal interviews with farmers. An indirect ELISA test was used to detect antibodies against B. besnoiti. Chi-square analysis and multivariable logistic regression model were used to identify risk factors associated with seropositivity to B. besnoiti. At the individual cow and herd level, the true prevalence of seropositive animals was 6 and 28.7 %, respectively. Cows between 2 and 6 years of age had significantly higher seroprevalence of B. besnoiti than other age groups. The highest seroprevalence of B. besnoiti was found in Zarqa and Irbid governorates. Multivariable logistic regression model identified that exchanging visits by farm workers to neighboring farms as a risk factor for seropositivity to B. besnoiti, while smaller herd size and twice a day farm cleaning using sweeping and water hosing were identified as protective factors. This is the first study that investigated the seroprevalence of B. besnoiti infection in dairy herds in Jordan. Further studies are warranted to explore the clinical manifestation of B. besnoiti infection as well as to identify the possible presence of other Besnoitia species and definitive hosts for the parasite.