The brain of all higher organisms has a modular architecture. Processing of various tasks, such as learning, olfaction, or motor control is performed in specialized brain areas, characterized by morphological and molecular peculiarities. To identify those genes that are transcribed in only one region of the insect brain, we chose two different approaches, differential display PCR and DNA array hybridization, with two different insect species, the desert locust Schistocerca gregaria and the fruitfly Drosophila melanogaster. The optic lobes (centers of visual information processing), the midbrain (the region of the brain where almost all "higher" centers are localized), and the thoracic ganglia (regions required to control various peripheral organs) were compared in both types of experiments. Both, the differential display PCR screen of the different parts of the locust brain as well as the DNA array screen of the Drosophila brain revealed almost identical numbers of transcripts exclusively present in either of the three above-mentioned brain areas. Interestingly, the brain areas with the largest number of differential transcripts are the thoracic ganglia and not the midbrain.