Currently, adult mesenchymal stem cells (MSCs) are being evaluated for a wide variety of therapeutic approaches. It has been suggested that MSCs possess regenerative properties when implanted or injected into damaged tissue. However, the efficacy of MSCs in several of the proposed treatments is still controversial. To further explore the therapeutic potential of these cells, it is necessary to trace the fate of individual donor or manipulated cells in the host organism. Recent studies from our lab showed that human placental alkaline phosphatase (hPLAP) is a marker with great potential for cell tracking. However, a potential concern related to this marker is its enzymatic activity, which might alter cell behavior and differentiation by hydrolyzing substrates in the extracellular space and thereby changing the cellular microenvironment. Therefore, the aim of this study was to characterize bone marrow MSCs (BMSCs) derived from hPLAP-transgenic inbred F344 rats (hPLAP-tg) in comparison to wild type (wt) BMSCs. Here, we show that BMSCs from wt and hPLAP-tg donors are indistinguishable in terms of cell morphology, viability, adhesion, immune phenotype, and proliferation as well as in their differentiation capacity over six passages. The expression of the hPLAP marker enzyme was not impaired by extensive in vitro cultivation, osteogenic, adipogenic, or chondrogenic differentiation, or seeding onto two- or three-dimensional biomaterials. Thus, our study underscores the utility of genetically labeled BMSCs isolated from hPLAP-tg donors for long-term tracking of the fate of transplanted MSCs in regenerative therapies.