Cytogenetic and molecular cytogenetic studies of individuals with autistic spectrum disorders indicate that 5-15% of them demonstrate chromosomal abnormalities that may be causative for these diseases. However, mosaic genetic alterations in autism remains to be studied. We have used interphase mFISH with chromosome enumeration DNA probes for chromosomes 1, 9, 13, 14, 15, 16, 17, 18, 21, 22, X and Y to determine the frequency of stochastic (or sporadic) aneuploidy and the presence of low level aneuploidy in lymphocytes in autistic patients and control group of non-autistic children. Through monitoring chromosome variations in a cohort of 24 individuals with autism and 18 matched controls we have detected that 8 cases of autism are characterized by low-level (4-12%) mosaic aneuploidy involving sex chromosomes (6 cases) and autosomes (2 cases). Since numerical chromosomal changes represent genome variations that affect whole gene set of a chromosome, it should be recognized that low-level chromosomal mosaicism could affect significantly development and functions of the brain without specific distinct clinical and phenotypic appearance. It is to note the difficulty to reveal mosaic chromosomal alterations by standard cytogenetic and molecular-genetic techniques without further application of molecular cytogenetics approaches. Our data suggest that interphase FISH is an adequate approach for identification of low-level chromosomal mosaicism in the diseased human somatic tissues. The work was supported by INTAS 03-51-4060 and RGRF (Russian Federation).