The quantification and analysis of the human transcriptome allows expanding the knowledge of the genomic functioning, especially in body’s parts as complex and important as the human brain. In this way, in silico studies offer the possibility to extract and analyse information contained in databases, at the level of gene expression along the different brain structures. This study aimed to correlate the transcription levels of 38 genes located in the critical region of the chromosome 21 associated with Down syndrome with the cerebral localization and its intervention in the correct operation of different brain substructures. To carry out this, the expression profiles of these genes along 24 substructures of the brain cores and 18 of the Limbic lobe were done, from gene expression data of microarray experiments of DNA, available in the database of the Atlas of the brain of the "Allen Institute for Brain Sciences". It was determined a differential expression of these genes along the analysed structures, in addition to register higher levels of overall transcription in certain areas of the brain, which appear to be associated with different processes of learning and memory. The differential transcription was correlated with the cerebral localization and its potential functional role.