Objective：To analyze the expression profile of lncRNA-mRNA in lesion and normal intestines of Hirschsprung’s diseases （HD）. Methods：The lncRNA-mRNA microarray was used to screen the differentially expressed lncRNA and mRNA in 5 HD intestines and 5 paired normal intestines. Seventeen groups of samples were used to do the quantitative real-time polymerase chain reaction（qRT-PCR） on 5 lncRNAs with significant differences. Gene co-expression network was constructed by bioinformatics methods. Results：There were 353 up-regulated and 474 down-regulated expression of lncRNA，and 865 up-regulated and 461 down-regulated expression of mRNA. lncRNA played a role in the pathogenesis of HD，by regulating the corresponding target mRNA，participating in various biological processes like cell proliferation，differentiation，migration et al. Conclusion：There are many differentially expressed lncRNA and mRNA in HD intestines. mRNA and lncRNA are closely related，forming co-expression network. lncRNA may participate in the pathogenesis of HD through regulating the corresponding target mRNA.