Mesenchymal stem cells (MSCs) have drawn great interest in the field of regenerative medicine, for cell replacement, immunomodulatory, and gene therapies. It has been shown that these multipotent stromal cells can be isolated from tissues such as bone marrow, adipose tissue, trimester amniotic tissue, umbilical cord blood, and deciduous teeth and can be expanded in adherent culture. They have the capacity to differentiate into cells of the connective tissue lineages in vitro and contribute to tissue parenchyma in vivo. However, proper in vitro manipulation of MSCs is a key issue to reveal a potential therapeutic benefit following transplantation into the patients. This chapter summarizes some of the essential protocols and assays used at our laboratory for the isolation, culture, differentiation, and characterization of mesenchymal stem cells from the bone marrow and adipose tissue.