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Background In the early postoperative period after pancreas-kidney transplantation, pancreatic venous thrombosis is a major complication that leads to allograft dysfunction and graft loss. Beside ischemia and reperfusion injury, immunosuppressive drugs have been accused of supporting thrombogenicity. The aim of this study was to evaluate the effect of commonly applied immunosuppressants on microvascular thrombus formation in normal and postischemic tissue in vivo. Methods In the skin fold chambers of tacrolimus-, cyclosporine A-, antithymocyte globulin-, rapamycine-, or saline-treated mice, light/dye-induced microvascular thrombus formation was studied. Additional mice underwent ischemia and reperfusion of the skin fold chamber tissue and received tacrolimus, antithymocyte globulin, or saline before reperfusion. Additionally, the effect of prednisolone was tested in animals with ischemia and reperfusion. Concentrations of sP-selectin, soluble vascular cell adhesion molecule-1, and asymmetric dimethylarginine were assessed by enzyme-linked immunosorbent assay. Immunohistochemistry of the skin fold chamber tissue served for analysis of vascular endothelial nitric oxide synthase and inducible nitric oxide synthase expression. Results In normal tissue, tacrolimus, cyclosporine A, antithymocyte globulin, and rapamycine accelerated microvascular thrombus formation significantly when compared with saline. Whereas ischemia and reperfusion in saline-treated mice enhanced thrombus formation, thrombogenicity was not further increased by ischemia and reperfusion in tacrolimus - or antithymocyte globulin-treated animals. Application of prednisolone reversed the tacrolimus- and antithymocyte globulin-induced prothrombotic effect. Antithymocyte globulin increased sP-selectin and soluble vascular cell adhesion molecule-1, whereas tacrolimus induced asymmetric dimethylarginine production significantly. While tacrolimus and antithymocyte globulin additionally induced endothelial nitric oxide synthase and inducible nitric oxide synthase expression, cyclosporine A influenced only endothelial inducible nitric oxide synthase expression. Conclusion Immunosuppressants enhance thrombus formation in vivo. Although antithymocyte globulin activates the microvascular endothelium, we show for the first time that tacrolimus increases asymmetric dimethylarginine plasma levels. Thus, impaired nitric oxide availability might be the underlying mechanism for the tacrolimus-associated increased thrombogenicity. The efficacy of prednisolone to reverse the tacrolimus-associated and antithymocyte globulin-associated acceleration of thrombus formation underlines the application of this anti-inflammatory drug prior to reperfusion in immunosuppressive regimens.