Alterations of the subchondral bone have been associated with the clinical use of marrow stimulation techniques for articular cartilage repair. Such changes that have also been described in small and large animal models of cartilage defects include modifications of the subchondral bone microarchitecture, the formation of intralesional osteophytes, the appearance of subchondral bone cysts and the upward migration of the subchondral bone plate. Their extent varies among the different animal models and operative techniques and over time. Although marrow stimulation procedures are important options to treat small symptomatic cartilage defects, these emerging experimental and clinical data suggest that a possible deterioration of the underlying subchondral bone plate and subarticular spongiosa might be an additional, previously underestimated factor that influences the long-term outcome of articular cartilage repair following marrow stimulation. A deeper comprehension of the subchondral bone alterations associated with cartilage repair techniques is therefore essential to preserve and restore the entire osteochondral unit. The aim of this review is to give an overview on the effect of marrow stimulation procedures on the subchondral bone, focusing on recent knowledge gained from experimental animal models and clinical investigations of subchondral bone alterations following marrow stimulation.