Methods of prolonging survival of a transplanted organ, as well as methods of preventing or attenuating rejection of a transplanted organ are provided. These methods involve contacting the organ with an inhibitor of complement activity (e.g., a complement inhibitor that has a maximum molecular weight of 70 kDa and/or a half-life shorter than 10 days, such as a CR2-FH fusion protein or a single chain anti-C5 antibody), prior to transplantation The methods also include administering to the allotransplant recipient an inhibitor of complement activity together with one or more immunosuppressants. A pretreatment with an alternative complement inhibitor was found to be effective in improving graft survival and decreasing ischemia-reperfusion injury in animal.