Bone marrow-derived mesenchymal stem cells (BM-MSC) are promising candidates for cell therapy and tissue engineering because they can be expanded in-vitro and induced to differentiate into many cell types. However, MSC’s are yet poorly described by genome-wide analyses. A better understanding of their regulatory physiology is required for manipulating them in vitro. Especially, we yet lack specific surface proteins that can be used to select MSCs for isolation from tissues. Therefore, a genome-wide transcription profile of BM-MSC was obtained using cDNA microarrays, with peripheral-blood mononuclear cells as a baseline. In addition, we combined a molecular tagging approach with the widely used gel-based MALDI-TOF, and also did a series of liquid chromatography-tandem mass spectrometry analyses (LC-MS/MS) on membrane fractions obtained by differential centrifugation to analyze the surface subproteome of MSC’s, in comparison to MSC-derived adipocytes. We found that genes that were highly expressed in BM-MSC’s, which we termed the MSC-related molecular profile, was similar to MSC’s from umbilical cord blood (UCB-MSC), but different from both hematopoietic stem cells (HSC) and embryonic stem cells (ESC). The membrane subproteome of MSC’s also revealed many candidate surface markers.