Induced pluripotent stem cell (iPSC) technology has great potential to establish novel therapeutic approaches in regenerative medicine and disease analysis. Although cell therapy using iPSC-derived cells still has many hurdles to overcome before clinical applications, disease analysis using patient-specific iPSCs may be of practical use in the near future. There are several reports that patient-specific iPSC-derived cells have recapitulated the apparent cellular phenotypes of a wide variety of diseases. Moreover, some studies revealed that it could be possible to discover effective new drugs and to clarify disease pathogenesis by examination of patient-specific iPSC-derived cells in vitro. We have recently reported that iPSCs can be a diagnostic tool in a patient with a novel mutation. For definitive diagnosis in a patient with long QT syndrome who had an uncharacterized genetic mutation, we succeeded in clarifying the patient’s cellular electrophysiologic characteristics and the molecular mechanism underlying the disease phenotype through the multifaceted analyses of patient-specific iPSC-derived cardiomyocytes. In this review, we focus on the conceptual and practical issues in disease modeling using patient-specific iPSCs and discuss future directions in this research field.