Acute mesenteric ischemia (AMI) is a rare condition that may be associated with a variety of congenital prothrombotic disorders (PDs). The purpose of this study was to assess the prevalence of these disorders in 28 AMI patients compared with 103 healthy individuals from the northeastern region of Turkey. They were screened for protein C, antithrombin 111, and protein S deficiencies; and gene analysis was performed using the polymerase chain reaction. A PD was revealed in 16 (57%) patients and 33 (32%) controls (p = 0.020). Factor V Leiden (FVL), prothrombin G20210A mutation, and TT677 homozygous mutation of methylenetetrahydrofolate reductase was detected in 10 (36%) patients versus 16 (15%) controls (p = 0.035), 3 (11%) patients versus 10 (9%) controls (p = 1.00), and 1 (3%) patient versus no controls, respectively. Consistent with caucasian ethnic groups, there was high prevalence of PDs, especially FVL; and these abnormalities might be a significant predisposing factor in the pathogenesis of AMI.