Background—Danon disease is an X-linked disorder that leads to fatal cardiomyopathy, caused by a deficiency in lysosome-associated membrane protein-2 (LAMP2). In female patients, a later-onset and less severe clinical phenotype have been attributed to the random inactivation of the X-chromosome carrying the mutant diseased allele. We generated a patient-specific induced pluripotent stem cell (iPSCs) based model of Danon disease to evaluate the therapeutic potential of Xi-chromosome reactivation using a DNA methylation inhibitor. Methods—Using whole exome sequencing, we identified a nonsense mutation (c.520CtextgreaterT, exon 4) of the LAMP2 gene in a family with Danon disease. We generated iPSC lines from somatic cells derived from the affected mother and her two sons, and then differentiated them into cardiomyocytes (iPSC-CMs) for modelling the histological and functional signatures, including autophagy failure of Danon disease. Results—Our iPSC-CM platform provides evidence that random inactivation of the wildtype and mutant LAMP2 alleles on the X-chromosome is responsible for the unusual phenotype in female patients with Danon disease. In-vitro, iPSC-CMs from these patients reproduced the histological features and autophagy failure of Danon disease. Finally, administration of DNA demethylating agent 5-aza-2’-deoxycytidine reactivated the silent LAMP2 allele in iPSCs and iPSC-CMs in female patients with Danon disease, and ameliorated their autophagy failure, supporting the application of a patient specific-iPSC platform for disease modeling and drug screening. Conclusions—Our iPSC-CM platform provides novel mechanistic and therapeutic insights into the contribution of random X-chromosome inactivation to disease phenotype in X-linked Danon disease.