iPS (induced pluripotent stem) cells can be induced from somatic cells in mice by genetic manipulation. Most previously established mouse IFS cell lines have been derived using feeder layers supplemented with exogenous LIF (leukaemia inhibitory factor). Although a feeder-free induction system has been developed in recent studies, LIF is still required for reprogramming, but its role in the generation of mouse iPS cells has remained elusive. In this study, we investigated its contribution to the induction of pluripotency. Our results showed that LIF activates AP (alkaline phosphatase) through a c-Myc-dependent mechanism. Moreover, it acts as a protective factor during the transition from AP-positive colonies to Oct3/4-positive cells. These findings illustrate a mechanism by which LIF may integrate signalling into reprogramming.