The CNVs identified in this study of individuals with neurodevelopmental disorders are rare and highly heterogeneous, with no single CNV being identified in more than 1% of the cases. Therefore, methods are needed to begin to statistically assess the relationship between such rare variation and human disease. For this study, we first focused on deletions and duplications of 14 recurrent genomic regions since their relative frequency is higher than CNVs involving non-recurrent regions. We selected 14 of the most common and clinically relevant recurrent CNVs (listed in Methods) for a formal case-control study to initiate an evidence-based process for defining the clinical significance of structural variation across the genome. Many of these 14 regions have inconclusive or contradictory data in the literature regarding their phenotypic implications, so a targeted analysis of these regions is needed to inform their functional significance.