In this study, hematoxylin-eosin(HE) staining, uranium acetate-lead citrate staining and immunohistochemical staining were used to analyses the effects of transport stress on morphology and three heat shock proteins expression(HSP27, HSP70 and HSP90) in mice immune organs(thymus, lymph nodes and spleen). The results showed that the thymus, lymph nodes and spleen of mice were all damaged by transport stress. The thymus medulla was enlarged and the blood vessels in the cortex were congested. The lymphatic nodules were shrinked and the splenic nodules were enlarged. The central artery was destroyed and cell apoptosis was showed up. The shape of lymphocyte nuclear membranes were performed as serration or even destroyed. A part of the nucleus of the eosinophilic granulocyte was disappeared. The destructive condition of the plasmocyte was even worse. The mitochondrial was swelled and cristae was damaged or disappeared. The expression of HSP27 in lymphoid nodule was gradually reduced, but that in medulla of lymph nodes and spleen were increased. In the medulla of lymph nodes, the expression of HSP70 was gradually reduced, but in lymphoid nodule and spleen red pulp were both increased. HSP90 was only obviously expressed in the lymph nodes. In summary, the transport induced stress would cause serious damages to the morphology of immune organs in mice, and the expression patterns of three stress related HSPs(HSP27, HSP70 and HSP90) were also changed. These results indicated that several certain regulatory relationships ware might exist between the HSPs and transport stress.