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Objective: In order to understand the role of long noncoding RNAs (lncRNAs) played in the mechanisms of glyphosate neurotoxicity in neuronal development. Methods: Perinatal glyphosate exposure (PGE) mouse model was constructed, and a lncRNA microarray was used to study the lncRNA expression changes in the hippocampus tissue of perinatal glyphosate exposure mice. Then we used GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases to analyze the function of the differentially expressed mRNAs and lncRNAs. Results: LncRNA microarray analysis revealed that 1759 lncRNAs and 759 mRNAs were differentially expressed in the perinatal glyphosate exposure (PGE) mice group (G group) compared with the normal control mice group (C group). The functions of the DEmRNAs are involved in the cellular response to hormone stimulus. The ceRNA analysis showed that some interaction networks existed, including (ENSMUST00000137546, ENSMUST00000160950)/(miR‐34a‐3p, miR‐130a‐3p)/(Il12b, Irf1). Further analysis of the target mRNAs of miRNAs indicated that the possible functions involved the neuroactive ligand‐receptor interaction and calcium signaling pathway, which are involved in perinatal glyphosate exposure‐induced neurotoxicity. Conclusion: The aberrant expression of lncRNAs is related to the perinatal glyphosate‐exposed neurotoxicity. These lncRNAs affect the target gene expression level, might by regulating neuroactive ligand‐receptor interactions. The (ENSMUST00000137546, ENSMUST00000160950)/ (miRNA‐34a‐5p, miR‐130a‐3p) / mRNAs (e.g., Il12b, Irf1) interaction network may functions in perinatal glyphosate exposure‐induced neurotoxicity. [ABSTRACT FROM AUTHOR]