Induced pluripotent stem (iPS) cells open new possibilities for autologous cell replacement therapies, establishment of human in vitro disease models, drug discovery and toxicology. However, before iPS cells can be used for any of these purposes the properties of their differentiated derivatives must be carefully examined. In this study we have compared functional and molecular properties of highly purified murine iPS and embryonic stem (ES) cell-derived cardiomyocytes (CM) generated from corresponding transgenic lines expressing puromycin N-acetyltransferase and green fluorescent protein under the control of a cardiospecific α-myosin heavy chain promoter. We demonstrate that murine iPS and ES cells differentiate into spontaneously beating CM at comparable efficiencies. Both iPS and ES cell-derived CM express typical cardiac transcripts and structural proteins and possess similar ultrastructural organization. Action potential recordings revealed that iPS- and ES cell-derived CM respond to adrenergic and muscarinic receptor modulation, express functional voltage-gated sodium, calcium and potassium channels and possess comparable current densities. Comparison of global gene expression profiles of CM generated from iPS and ES cells revealed that both cell types express genes and functional categories typical for CM and cluster close to each other but are highly distant to undifferentiated ES or iPS cells as well as unpurified iPS and ES cell-derived embryoid bodies (EB). These data suggest that iPS CM obtained by lineage selection are highly similar in their structure, function and molecular characteristics to CM derived from ES cells and may represent a valuable and safe source of cells for a variety of in vitro and in vivo applications. Similar findings have also been obtained in comparative studies of microdissected human ES cell- and iPS cell-derived CM.