Abstract: Hippocampus is a brain region mainly composed by neuron layers described as Dentate Gyrus(DG) and Ammon’s horn(CA). This study explores the differential transcripts datasets of hippocampal layers (CA1, CA2, CA3, DG) for elucidating their distinctions. All layers were bilaterally collected from hippocampus of each rat, total RNA was extracted, and libraries for RNA-Seq in Illumina Hiseq platform were prepared according to manufacturer instructions. Sequences were aligned and quantified with the STAR Aligner/DESeq2 pipeline. Gene Onthologies were analyzed with the DAVID software. In results, CA1 neurons are expressing more genes related to circadian rhythms, postsynaptic membrane receptors that are important for manutence of excitability, learning and memory. In CA2 and CA3 were found transcripts associated to higher metabolic pathways demand and endocytosis recycling. Dentate gyrus neurons expression was related to ribosome, spliceosome, essential for protein synthesis that supports dendritic growth and maintenance of long-term potentiation. These findings yield new information into specific molecular alterations in hippocampus layers which contribute to understanding the singularity of hippocampal formation Ver menos