This dataset was generated using the SNP-array technique, applied to 48 patients with malformations of cortical development (MCDs). The method enables the detection of structural genomic alterations, particularly copy number variations (CNVs) and regions of homozygosity (ROH), providing a complementary perspective to exome sequencing for the characterization of genetic etiology. Samples were processed with the CytoScanHD kit (Affymetrix/Thermo Fisher Scientific) and scanned on the GeneChip®️ Scanner 3000 7G, following validated manufacturer protocols. Data were analyzed using the Chromosome Analysis Suite (ChAS, hg19) software. CNV calling followed manufacturer thresholds, with filters of 25 probes for deletions, 50 for duplications, and 100 kb minimum size. Variants were classified by comparison with control datasets and reference databases, including DGV, DECIPHER, ClinGen, and OMIM, with additional validation using secondary methods when requiredhe resulting dataset contributes to elucidating the genetic basis of MCDs and enhances understanding of the molecular mechanisms underlying neurological conditions such as epilepsy, developmental delay, and intellectual disabilityuch as epilepsy, developmental delay, and intellectual disability.