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Background: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with strong genetic underpinnings. Microarray‐based comparative genomic hybridization (aCGH) technology has been proposed as a first‐level test in the genetic diagnosis of ASD and of neurodevelopmental disorders in general. Methods: We performed aCGH on 98 Tunisian children (83 boys and 15 girls) diagnosed with ASD according to DSM‐IV criteria. Results: "Pathogenic" or "likely pathogenic" copy number variants (CNVs) were detected in 11 (11.2%) patients, CNVs of "uncertain clinical significance" in 26 (26.5%), "likely benign" or "benign" CNVs were found in 37 (37.8%) and 24 (24.5%) patients, respectively. Gene set enrichment analysis involving genes spanning rare "pathogenic," "likely pathogenic," or "uncertain clinical significance" CNVs, as well as SFARI database "autism genes" in common CNVs, detected eight neuronal Gene Ontology classes among the top 10 most significant, including synapse, neuron differentiation, synaptic signaling, neurogenesis, and others. Similar results were obtained performing g: Profiler analysis. Neither transcriptional regulation nor immune pathways reached significance. Conclusions: aCGH confirms its sizable diagnostic yield in a novel sample of autistic children from North Africa. Recruitment of additional families is under way, to verify whether genetic contributions to ASD in the Tunisian population, differently from other ethnic groups, may involve primarily neuronal genes, more than transcriptional regulation and immune‐related pathways. [ABSTRACT FROM AUTHOR]