It has recently been shown that adipose tissue is an abundant and easily accessible source of stromal progenitor cells (ADSCs, adipose-derived stromal cells), resembling the mesenchymal stem cells (MSCs) obtained from adult bone marrow. However, the identification of these two lineages is still controversial and even the stem cell nature of ADSCs is doubted. In this study, we examined the "stemness" transcriptional profile of ADSCs and BM-MSCs, with two aims: (1) to compare their "stem cell molecular signature" and (2) to dissect their constitutive expression pattern for molecules involved in tissue development, homeostasis and repair. As well as several molecules involved in matrix remodeling and adult tissue angiogenesis and repair, we detected the expression of genes UTF-1, Nodal, and Snail2, which are known to be expressed by embryonic stem cells but have been never described in other stem lineages. In addition, for the first time we described the transcriptional profile of human BM-MSCs and ADSCs for the CD44 splice variants, which are determinant in cell trafficking during embryonic development, in adult tissue homeostasis and also in tumor dissemination. Thus, our findings strongly support a close relationship between ADSCs and BM-MSCs, suggest an unexpected similarity between MSCs and embryonic stem cells, and possibly support the potential therapeutic application of ADSCs.