Most of the plant shoot originates from a small group of stem cells, which in Arabidopsis are specified by WUSCHEL (WUS). It is unknown whether these cells have an intrinsic potential to generate shoot tissues, or whether differentiation is guided by signals from more mature tissues. Here we show that WUS expression in the root induced shoot stem cell identity and leaf development (without additional cues), floral development (together with LEAFY), or embryogenesis (in response to increased auxin). Thus, WUS establishes stem cells with intrinsic shoot identity and responsive to developmental inputs that normally do not change root identity.