Balanced differentiation of mesenchymal stromal cells (MSCs) into osteoblasts and adipocytes is essential for healthy bone and fat homeostasis. A disturbed balance of MSC differentiation results in bone loss and increased adipogenesis as observed in several human conditions, such as osteoporosis, obesity, and aging. This reflects the importance of MSC fate decision. Therefore, it is important to identify factors that regulate the balance between osteogenic and adipogenic differentiation of MSCs so as to identify new targets to improve bone formation in osteoporosis and control adipose tissue development. There is accumulating evidence that thymus cell antigen 1 (Thy‐1), also known as CD90, expressed on MSCs, plays a critical role in the fate decision of MSCs. Recently, Thy‐1 has been shown to promote osteogenic differentiation of MSCs and thus bone formation while inhibiting adipogenic differentiation and restricting adipose tissue accumulation. The clinical importance of these findings was validated by the detection of reduced serum soluble Thy‐1 in patients with disturbed bone remodeling. In this review, we aim to summarize data on the impact of Thy‐1 on the control of MSC differentiation and its consequences for bone and fat formation.—Saalbach, A., Anderegg, U. Thy‐1: more than a marker for mesenchymal stromal cells. FASEB J. 33, 6689–6696 (2019). http://www.fasebj.org