Labelling of mammalian cells with superparamagnetic iron oxide (SPIO) nanoparticles enables to monitor their fate in vivo using magnetic resonance imaging (MRI). However, the question remains whether or not SPIO nanoparticles affect the phenotype of labelled cells. In the present study, the effects of SPIO nanoparticles from two producers on the growth and differentiation of mouse embryonic stem (ES) cells in vitro were investigated. Our observations have shown that SPIO nanoparticles have no effect on the self-renewal of ES cells. Subsequently, we studied the effect of SPIO on the formation of embryoid bodies and neural differentiation of ES cell in monolayer culture. The cavitation of embryoid bodies was partially inhibited and neural differentiation was supported regardless the type of SPIO nanoparticles used. Thus for the first time we documented the effects of SPIO nanoparticles on ES cells and their differentiation.