Abstract <p>Over the past 6–8 million years, in the evolutionary line leading to modern humans, the brain has undergone significant changes. Its volume has tripled compared to that of other great apes, and the increased structural complexity has been associated with a marked prolongation of developmental stages. The emergence of these specific morphological features is linked to profound alterations in the genetic programs regulating brain development. Changes in regulatory regions of the human genome, which can modify the spatiotemporal patterns of gene expression, have a significant impact on this evolutionary process. One of the drivers of such evolutionary changes is human accelerated regions (HARs), which represent conserved DNA regions in mammals that have acquired specific mutations in humans. The overwhelming majority of these elements are non-coding DNA sequences, localized in intronic and intergenic regions near genes essential for brain development. Genetic variants within HARs have been associated with neurodevelopmental and psychiatric disorders and are known to alter gene expression. One gene whose regulation may be influenced by HARs is <i>CNTN6</i>. Two HARs have been identified within its introns and frequently overlap with <i>CNTN6</i> copy number variations observed in patients with neurodevelopmental disorders. To further investigate the functional role of one of these elements, HARsv2_1747, in human neurodevelopment, we used the CRISPR/Cas9 system to generate two human induced pluripotent stem cell (iPSC) lines: one with a homozygous deletion and another with a compound heterozygous deletion of this region. Both iPSC lines fulfill the key criteria for pluripotency, as they form colonies with typical pluripotent cell morphology, maintain a normal diploid karyotype, express pluripotency markers, and retain the ability to differentiate into derivatives of all three germ layers.</p>