In this study, we demonstrate that we can isolate stem cells (SCs) with neural crest characteristics from the bulge area of cultured human hair follicles (HFs). These SCs can proliferate in situ and form spheroid structures attached to the bulge area of HFs, and they express immature neural crest cell markers but not differentiation markers. An expression profiling study showed that they share a similar gene expression pattern with murine skin immature neural crest cells. These human SCs are label-retaining cells and are capable of self-renewal through asymmetric cell division in vitro. They exhibit clonal multipotency that can give rise to myogenic, melanocytic, and neuronal cell lineages after in vitro clonal single cell culture. In addition, these SCs show differentiation potential toward mesenchymal lineages, and they can be differentiated into adipocyte, chondrocyte, and osteocyte lineages. Neuronal differentiation of these cells induces global gene expression changes with a significantly increased expression of neuron-associated genes. Differentiated neuronal cells can persist in mouse brain and retain neuronal differentiation markers. The presence of SCs with neural crest characteristics in HFs may offer new opportunities for the use of these cells in regenerative medicine.