Red blood cell transfusion is required for many types of surgery against cardiovascular disease, and the function of transfused cells appears to decline over time. The present study examined whether transfusion also reduces red blood cell lifespan in a rat model. Bypass in rats were established by connecting a roll pump to the femoral artery and vein. Then FITC-labeled stored red blood cells from rats were transfused in the animals, and the cells in circulation were counted after transfusion. In separate experiments, stored red blood cells were incubated with bypass plasma in vitro, and the effects of incubation were assessed on cell morphology, redox activity, ATP level, caspase-3 activity, and phosphatidylserine exposure on the cell surface. These in vivo and in vitro experiments were also performed after pretreating the stored red blood cells with the caspase-3 inhibitor Z-DEVD-FMK. Bypass significantly decreased the number of circulating FITC-labeled stored red blood cells and increased the proportions of monocytes, neutrophils and splenic macrophages that had phagocytosed the red blood cells. In vitro, bypass plasma altered the morphology of red blood cells and increased oxidative stress, caspase-3 activity and phosphatidylserine exposure, while decreasing ATP level. Pretreating stored red blood cells with Z-DEVD-FMK attenuated the effects of bypass on caspase-3 activity, but not oxidative stress, in stored red blood cells. Bypass appears to shorten the lifespan of stored red blood cells, at least in part by activating caspase-3 in the cells.