Waardenburg syndrome (WS) is a genetic disorder characterized by sensorineural deafness. It has a variable presentation of pigmentation defects. Here, we generated an induced pluripotent stem cell (iPSC) line using episomal plasmid vectors from the fibroblasts of a 4-year-old boy affected with WS type II, caused by a novel mutation in microphthalmia-associated transcription factor (MITF) (NM_000248.3: exon6:c.626A>T). The patient-specific iPSC line (CSUXHi003-A) carrying the same MITF mutation showed normal karyotype, expressed pluripotent markers, and presented differentiation capacity in vitro. It may be a useful tool for in vitro modeling of WS.