The present invention relates to a bone regeneration or bone formation promoting pharmaceutical composition comprising muramyl dipeptide, an analog thereof, a derivative thereof or a pharmaceutically acceptable salt thereof. In contrast to existing passive therapeutic agents which center on bone absorption suppression based on mechanisms for reducing osteoclast functionality, the composition comprising muramyl dipeptide of the present invention promotes the differentiation of osteoblasts, which are bone forming cells, and can advantageously be used in various diseases where bone formation is required as an active therapeutic agent that does not affect osteoclast.