Autism is a neurodevelopmental disorder characterized by clinical, etiologic and genetic heterogeneity. It is often associated with other conditions, such as disorders of the CNS (tuberous sclerosis), developmental delay, attention deficit, epilepsy, and anxiety and mood disorders. Our survey found cytogenetically visible chromosomal anomalies in ∼7.4% (129 / 1749) of autistic patients documented as well as several sub-microscopic variants. Almost every chromosome is affected by numeric or structural aberrations. Among the most consistent cytogenetics findings are fragile X and duplication of maternal 15q11-q13. Molecular cytogenetics, together with genome scans and linkage / association studies, point to ≥22 chromosome regions harbouring putative autism susceptibility genes, such as 2q32, 3q25-q27, 7q31-q35, 15q11-q13, 16p13, Xp22, and Xq13. We hypothesize that there might be at least three types of autism susceptibility genes / mutations that can be (i) specific to an individual patient or family, (ii) in a genetically isolated sub-population and (iii) a common factor shared amongst different populations. The genes / mutations could act alone or interact with other genetic and / or epigenetic or environmental factors, causing autism or related disorders. This review emphasizes the potential of analysing chromosomal rearrangements as a means to rapidly define candidate disease loci for further investigation. To facilitate ongoing research we have established a new database of autism-associated chromosomal anomalies (http: / / tcag.bioinfo. sickkids.on.ca / autism).