A 2-year-old boy who was failing to thrive and who had multiple anomalies was found to have a maternally derived tandem duplication of the long arm of the X chromosome: dup(X)(q13.2-q21.2). The karyotyping interpretation was further confirmed by fluorescence in situ hybridization studies in which a double gene dosage of the X-inactivation-specific transcript (gene locus on Xq13.2) and a whole chromosome X painting on the abnormal X were noted. He suffered from hypotonia, gastroesophageal reflux, laryngomalacia, recurrent infections, immunodeficiency (IgG4 deficiency), dysgenesis of the corpus callosum, proximal renal tubular acidosis, and nephrolithiasis. His mother and elder sister also had the same rearrangement, the dup(X), on one of their X chromosomes. However, the mother was in good health, but the sister suffered from nephrolithiasis. The clinical variability in this family with the Xq duplication is reported and discussed.