Proper functioning of the nervous system is largely dependent on the precise regulation of the neuronal environment. By shielding the central nervous system (CNS) from potentially harmful substances, the blood-brain barrier (BBB) has an indispensable role in this process. The BBB is a specialized system of endothelial cells lining brain microvessels, which – supported by pericytes and glial cells – form a selective barrier between the blood and the neural tissue. Under abnormal conditions, permeability of the BBB may increase, which may either trigger or aggravate the disease. Since CNS disorders – at least in their initial phase – usually do not involve the whole brain and spinal cord, but are localized to a certain region, our aim was to understand whether the BBB is regionally heterogeneous at the molecular level. By using bioinformatics tools, we analyzed expression levels of genes specific to cerebral endothelial cells, pericytes or astrocytes in different brain territories. Our results revealed regional heterogeneities in the expression of BBB-associated genes in both human and mouse. Expression pattern of efflux transporters – which have a major role in blocking passage of therapeutic agents through the BBB – proved to be diverse both among brain regions and between mouse and human. Our results indicate that: (1) in silico database analyses are suitable for group-based studies on gene functions, overcoming the limitations of single-gene analyses; (2) high-throughput tests should always be validated using other methods; (3) when using animal models, inter-species differences have to be always considered; (4) when comparing different brain regions, the BBB is heterogeneous at the molecular level, and this might have clinical significance.