The transcription factor Helios has been reported to be a marker of regulatory T cells (Treg) of thymic origin, distinguishing them from Treg induced in the periphery (iTreg). In this study, we demonstrate Helios expression in Foxp3+ iTreg, both in vitro and in vivo. Following iv peptide injection, in vivo Helios expression in adoptively transferred TCR transgenic T cells was more rapid than Foxp3 induction but less stable at later time points without a second injection of peptide. Our in vitro data suggest that APC influence Helios expression in a manner distinct from stimuli required for Foxp3 induction. Thus, Helios expression in iTreg may reflect the context of stimulation during Foxp3 induction. In summary, the robust Helios expression we observe in iTreg precludes its use as a marker of thymic Treg.