Capturing the complexity of bone and cartilage into three-dimensional in vitro models remains one of the most important challenges in the field of the tissue engineering. Indeed, the development and the optimization of novel culture systems may be necessary to face the next questions of bone and cartilage physiology. The models should faithfully mimic these tissues, resembling their organization, their mechanical properties and their physiological response to different stimuli. Here we review the recent advances in the field of the three-dimensional cultures of both osteogenic and chondrogenic cells. In particular, we highlight the most important studies that, to our knowledge, have investigated the response of the cells to the three-dimensional environment provided by the diverse types of scaffold.