Ataxia-telangiectasia (A-T) is an inherited neurodegenerative disease manifested in childhood and associated with neuronal death, cancer predisposition and premature aging. Genome (chromosome) instability is one prominent feature of A-T. Markedly increased level of tissue-specific chromosomal rearrangements and aneuploidy has been demonstrated in lymphocytes and fibroblasts of A-T. Therefore, it is reasonable to propose that neurons in human A-T brain could also have altered chromosomal complement and, probably, should demonstrate increased frequency of aneuploidy. However, direct proof of this hypothesis needs to be provided. The present study of autopsy brain tissues demonstrates the validity of multicolor FISH and Multicolor Banding for interphase chromosome complement variations in the brain. A 2-4-fold increase of aneuploid neuronal and glial cell frequency has been detected in the A-T brain as to postmortem brain tissues of age-matched control. Therefore, we suggest that neuronal chromosome pathology is the primary cause of the loss of neurons in the A-T brain and, therefore, should be primarily taken into account for the treatment of neurodegeneration and premature aging of the brain. This implies for the necessity of interphase FISH for developing of efficient approaches to uncover chromosome instability in postreplicative cells of somatic tissues in neurodegenerative diseases. The work was supported by INTAS 03-51-4060 and A-T Children’s Project.