Apoptosis in organs of rats in early stage after polytrauma combined with shock was researched. Sixty Sprague-Dawley rats were divided into six groups: normal control (A, n = 6), sham-operation (N, n = 6), single hemorrhagic shock (S, n = 6), two-site trauma/shock (B, n = 6), four-site trauma/shock (C, n = 6), and six-site trauma/shock (D, n = 30). Shock was kept 60 min by blood withdrawal. Polytrauma was performed by clamping different sites of limbs to make fractures according to different groups: B at both femurs; C at femurs and tibias; and D at femurs, tibias, and humeri. The animals of A were totally normal without any operation. The rats of N, S, B, and C were killed at 6 hours after resuscitation, and the rats of D were killed at 1, 3, 6, 12, and 24 hours, respectively. Then, DNA agarose gel electrophoresis, in situ end-labeling (ISEL), and light and electron microscopy were performed and the percentage of DNA fragmentation was detected to assess apoptosis. In B, C, and D, the special ladder patterns for apoptosis were seen in thymus, spleen, liver, lung, and intestine, but not in heart, kidney, and brain. However, positive responses were observed in all these eight organs by ISEL. At 6 hours after resuscitation, the percentages of DNA fragmentation in thymus, spleen, liver, lung, and intestine all increased together with the severity of trauma. In D, the percentages of DNA fragmentation in these five organs all increased significantly at 1 hour after resuscitation. At 3 hours, the percentages in spleen, liver, lung, and intestine reached peak, and declined gradually afterward, whereas those in thymus continued increasing after 3 hours and kept stable from 6 hours to 24 hours. It was shown by morphologic examination that the majority of apoptotic cells lay in cortex of thymus, in growth center of white pulp of spleen, in border area of hepatic lobule and portal area of liver, and at the base of crypts of intestine. In lung, multiple kinds of cells, including alveolar epithelial cells, vascular endothelial cells, and polymorphonuclear neutrophils, induced apoptosis. Apoptosis was induced in thymus, spleen, liver, lung, and intestine in early stage after polytrauma combined with shock, which may play partial roles in the development of multiple organ failure.