--- - |2+ Background Williams syndrome (WS) is a neurodevelopmental disorder that has been attributed to heterozygous deletions in chromosome 7q11.23 and exhibits a variety of physical, cognitive, and behavioral features. However, the genetic basis of this phenotypic variability is unclear. In this study, we identified genetic clues underlying these complex phenotypes. Methods Neurobehavioral function was assessed in WS patients and healthy controls. Total RNA was extracted from peripheral blood and subjected to microarray analysis, RNA‐sequencing, and qRT‐PCR. Weighted gene co‐expression network analysis was performed to identify specific alterations related to intermediate disease phenotypes. To functionally interpret each WS‐related module, gene ontology and disease‐related gene enrichment were examined. We also investigated the micro (mi)RNA expression profiles and miRNA co‐expression networks to better explain the regulation of the transcriptome in WS. Results Our analysis identified four significant co‐expression modules related to intermediate WS phenotypes. Notably, the three upregulated WS‐related modules were composed exclusively of genes located outside the 7q11.23 region. They were significantly enriched in genes related to B‐cell activation, RNA processing, and RNA transport. BCL11A, which is known for its association with speech disorders and intellectual disabilities, was identified as one of the hub genes in the top WS‐related module. Finally, these key upregulated mRNA co‐expression modules appear to be inversely correlated with a specific downregulated WS‐related miRNA co‐expression module. Conclusions Dysregulation of the mRNA/miRNA network involving genes outside of the 7q11.23 region is likely related to the complex phenotypes observed in WS patients. - Journal of Child Psychology and Psychiatry, EarlyView.