In the non-heart-beating donor (NHBD) deterioration of microcirculation of the liver graft is strongly associated with secretion of cytokines and eicosanoids. In this study we investigated the excretion of cytokines, eicosanoids, and DNA binding activity of transcription factors in the grafts from NHBD and evaluated the effects of the elimination of Kupffer cells on them. The purpose of this study was to clarify the impact of Kupffer cells on transcription factor activity and the that of cytokine and eicosanoid production on reperfusion injury of liver grafts from NHBD. Wistar rats were allocated to four groups: (a). control group: livers were extracted under heart-beating conditions and perfused without cold storage, (b). heart beating (HB) group: livers extracted under heart-beating conditions were perfused after 6 h of cold storage, (c). non-heart-beating (NHB) group: livers extracted after cardiac arrest were perfused after cold storage, (d). Kupffer cell eliminated (KE) group: liposome-encapsulated dichloromethylene diphosphonate was intravenously administered to eliminate Kupffer cells before extraction, and the liver was perfused after cold storage. Cytokines and eicosanoids in perfusate were measured. DNA binding activity of nuclear factor kappa B, activating protein 1, and nuclear factor-interleukin 6 of tissue were investigated. Concentrations of interleukin 1 beta and thromboxane B(2) in the perfusate were significantly higher in NHB group, but they were completely suppressed in the KE group. A rise in binding activity of nuclear factor kappa B and activating protein 1 was not observed during cold storage in any groups, but these activities did increase remarkably after reperfusion. Significant buildup of those activities were recognized in the NHB group, and this phenomenon was inhibited in the KE group. The histological structures of the sinusoid in the KE group were well maintained, as with those of the control group. These results indicate that cytokines, eicosanoids, and the DNA binding activity of the transcripton factor are strongly associated with reperfusion injury, and Kupffer cells play an important role in this mechanism in grafts from NHBDs.