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Recent advances in Next-Generation Sequencing (NGS) technologies have revolutionized the field of human genetics. Alongside a broad panel of bio-informatics tools and databases, NGS technologies have unprecedentedly improved the molecular diagnosis rate and the identification of new genes associated with rare disorders. However, about 50% of patients remain without a final diagnosis. Here, we highlight the utility of NGS applications in developmental anomalies and intellectual disability, illustrating their main advantages and pitfalls.