Nutritional trace element selenium（Se）is a valuable component for the normal immune function in various life forms.Selenoproteins and Se play important roles in the immune system.Se is necessary for the immune system in chicken and mediates its physiological functions through selenoproteins.Cytokines are soluble,low molecular weight polypeptides and glycopeptides produced by a broad range of cell types of haematopoietic and nonhaematopoietic origin that have suppressive or enhansive effects on cellular proliferation,differentiation,activation,and motility.Heat shock proteins（Hsps）are present nearly in all species with their conserved nature,and Hsps are used as biomarkers of various stresses condition in animals as well as birds.Autophagy is a process which exerts effect of targeted component and its action in particular cells and system.Selenoprotein,cytokine,Hsps,autophagy related genes and ultra structures in the immune system of mammals are sensitive to dietary Se levels;however,little is known about the expression of selenoproteins,Hsps mRNAs,Hsp proteins level,mRNAs expression of autophagy-related genes,protein levels of autophagy-related genes,effects on cytokines,and on internal structures of in the chicken spleen,bursa of Fabriciuos and thymus with Se deficiency.We assessed selenoproteins mRNAs expression of（Txnrd1,Txnrd2,Txnrd3,Dio1,Dio2,Dio3,GPx1,GPx2,GPx3,Gpx4,Seppl,Selo,Sep 15,Sepx1,Sets,Setli,Selu,Selh,and SPS2）,Hsps mRNAs expression of（Hsp27,Hsp40,Hsp60,Hsp70,and Hsp90）,Hsp proteins level of（Hsp40,Hsp60,Hsp70,and Hsp90）,autophagy-related genes mRNAs expression of（LC3-Ⅰ,LC3-Ⅱ,Beclin 1,Dynein,ATG5,TOR1）,protein levels of autophagy related genes（LC3-Ⅱ,Beclin 1,Dynein）,cytokine content（IL-2,IL-6,IL-8,IL-10,IL-17,IL-1β,IFN-α,IFN-β,IFN-γ and TNF-α）and change in structural integrity in the tissues in the chicken spleen,bursa of Fabricius and thymus in this study.The animals were randomly assigned into two groups as follows:the Se-deficient group（L group）was fed a diet containing 0.033 mg Se/Kg,and the control group was fed the same basal diet supplemented with Se at 0.15 mg/kg（sodium selenite）.Real-time qPCR was used to investigate the expression level of selenoproteins,Hsps and autophagy-related genes on days 15,25,35,45,and 55,protein level of heat shock protein and autophagy genes were check through western blot analysis on days 35,45 and 55,ELISA was used to evaluate the cytokine content on days 15,35,and 55,an electron microscope was used to observed the structural change in chicken immune organs.The result revealed that selenoprotein messenger RNA（mRNA）levels of Txnrdl,Txnrd2,Txnrd3,Dio1,Dio2,Dio3,GPx1,GPx2,GPx3,Gpx4,Sepp1,Selo,Sep15,Sepx1,Sels,Seli,Selu,Selh,and SPS2 were all significantly decreased in the Se deficiency group compared to the control group in spleen,bursa of Fabricius and thymus of chicken.Cytokines study showed that in spleen IL-2,IL-6,IL-17,IL-1β,IFN-α were significantly decreased and there was also significant increased in IL-8,IL-10,IFN-β,IFN-y and TNF-a in Se deficiency group.In bursa of Fabricius the IL-2,IL-6,IL-8,IL-10,IL-17,IL-β,IFN-α,IFN-β,IFN-γ were significantly decreased,and TNF-a was significantly increased in the Se deficiency.In thymus a significant decrease in IL-2,IL-10,IL-17,IL-1β,IFN-α,IFN-β was observed in the Se deficiency group,and there also a significant increase in IL-6,IL-8,IFN-1γ,and TNF-α in the L group in thymus of chicken.Result of Hsps messenger RNA（mRNA）levels showed that（Hsp27,Hsp40,Hsp60,Hsp70,and Hsp90）were significantly increased in spleen,bursa of Fabricius and thymus of the Se deficient group.The proteins levels of Hsps（Hsp60,Hsp70,and Hsp90）were significantly increased in spleen,bursa of Fabriciuos and thymus of the Se deficient group.Autophagy-related gene expression results showed that in spleen mRNA levels of LC3-Ⅰ,LC3-Ⅱ,Beclin 1,Dynein,ATG5,TOR1 were high and protein levels LC3-Ⅱ,Beclin 1 and Dynein was also observed high in Se deficiency group as compared to control group in chicken spleen.In bursa of Fabricius as compared to the control group mRNA level of LC3-Ⅰ,LC3-Ⅱ,Beclin 1,Dynein,ATG5,TOR1 was increased and protein level of Beclin 1 and Dynein were increased and LC3-2 was low in Se deficiency group.In thymus as compared to the control group mRNA levels of LC3-Ⅰ,Beclin 1 and AGT5 were high and LC3-Ⅱ,Dynein,TORlwere observed low and protein level of Beclin 1 was high and LC3-Ⅱ and Dynein were recorded low in Se deficiency group.Further cellular morphological changes such as autophagy vacuole,autolysosome and lysosomal degradation were observed in the spleen,bursa of Fabricius and thymus of Se deficiency group.In summary,Se deficiency results in significant decreased in the expression of selenoproteins,change in the cytokine,and change in autophagy-related genes.Further ultra structure in chicken immune organs showed histopathology,immuno-supersion,and increased in the Hsps participated in protective mechanism in tissues of spleen,bursa of Fabricius and thymus of Se deficiency group.Our results provide a comprehensive tool of structural injuries in the chicken immune organs with Se deficiency.