Intellectual disability and autism spectrum disorders resulting from MECP2 gene alterations, such as Rett syndrome (RTT) and MECP2-duplication syndrome (MDS), present challenges in understanding the complex links between genetic alterations and cognitive deficits. Previous animal-based studies, though insightful, face translational barriers due to evolutionary differences in brain development between species, hindering direct application to humans.To address this, we established an innovative in vivo human neuronal model for RTT and MDS, utilizing patient-derived induced pluripotent stem cells (iPSCs) differentiated into cortical neurons. This model enables the in vivo study of MECP2 alterations' impact on human neurons, providing a comprehensive understanding of cellular and molecular changes during development.Our study integrates single-nucleus RNA sequencing (snRNAseq) with detailed analyses of neuronal morphology, including Sholl analysis and spine quantification. snRNAseq reveals distinct transcriptional profiles in MECP2-mutant neurons, exposing gene expression alterations underlying observed phenotypes. Simultaneously, morphological assessments offer insights into structural consequences during human neuronal development.These analyses deepen our understanding of pathophysiological mechanisms in MECP2-related disorders, establishing a platform for evaluating potential therapeutic interventions. Our approach, combining advanced molecular techniques with morphological assessments, contributes to unraveling complexities in genetic neurodevelopmental disorders, aiding the development of targeted treatments.Figure Patient-derived iPSCs differentiate into cortical neurons (Day 0-27). Transplantation into RAG2KO mice (Day 40 – P0). Integrated cortical neurons are studied longitudinally 1-7 months post transplantation (MPT) at the structural and molecular levels.