Hippocampal sclerosis (HS) is the most common surgical pathology associated with temporal lobe epilepsy (TLE). However, the cause of TLE with or without HS remains unknown. Our current study aimed to illustrate the essential molecular mechanism that are potentially involved in the pathogenesis of TLE-HS and to shed light on the transcriptional changes associated with hippocampal sclerosis. RNA-seq analysis was performed to evaluate profiling of circRNAs and mRNAs in hippocampal tissues of HS IALE-type 1 and no-HS patients. Systematic bioinformatic analysis of expression levels was utilized in circRNAs and mRNAs. Altered expression of selected circRNAs and mRNAs levels was confirmed by RT-PCR. In this study, we explored transcriptomic profiling of circRNAs and mRNAs expression in 3 ILAE type 1 and 3 no-HS hippocampal tissues.Compared to no-HS group, 341 mRNA transcripts and 133 circRNA transcripts were differentially expressed in ILAE type 1 group. Gene Ontology analysis demonstrated that the dysregulated genes were associated with the biological processes of vesicle-mediated transport. Enrichment analysis demonstrated that dysregulated genes were involved mainly in the mitogen-activated protein kinase (MAPK) signal pathway. Subsequently, A total of 441 known or predicted interactions were formed among DEGs, and the most important module was detected in the PPI network using the MCODE plug-in. There were mainly four functional modules enriched: ER to Golgi transport vesicle membrane, Basal transcription factors, GABA-gated chloride ion channel activity, CENP-A containing nucleosome assembly. A circRNA-mRNA co-expression network was constructed including 5 circRNAs(hsa_circ_0025349, hsa_circ_0002405, hsa_circ_0004805, hsa_circ_0032254, and hsa_circ_0032875) and three mRNAs (FYN, SELENBP1, and GRIPAP1)based on the normalized mRNA signal intensities. This is the first to report the circRNAs and mRNAs expression profile of surgically resected hippocampal tissues from TLE patients of ILAE-1 and no-HS, and these results may provide new insight on the transcriptional changes associated with this pathology.