Osteoarthritis (OA) is a degenerative disease that is characterized by joint discomfort, loss of articular cartilage, and changes to the subchondral bone. Studies to elucidate the pathophysiology of OA have been hampered by the lack of a rapid, reproducible animal model that mimics the structural changes associated with the disease. A single intra-articular injection of mono-iodoacetate (MIA), an inhibitor of glycolysis, into the femorotibial joint of rodents promotes loss of articular cartilage similar to that noted in human OA. The purpose of the present study was to determine whether in vivo three-dimensional micro computed tomography (microCT) was of use for detecting progressive changes over time to the subchondral bone (femorotibial joint) of Wistar rats treated with a single intra-articular injection of MIA. MIA-treated right knee joints and left contralateral control knee joints were imaged in vivo at 0, 1, 7, 14, 28, and 56 days postinjection by using microCT. Analysis of 50- and 100- micro m resolution images demonstrated that changes to the subchondral bone, as determined by visual and bone mineral density analysis, are apparent by day 14 post-MIA. By day 28, there were marked changes to lateral aspect of the medial tibial plateaus of the subchondral bone in MIA-treated joints. These changes were progressive through day 56. It was concluded that intra-articular injection of MIA induces progressive changes to subchondral bone that can be assessed using in vivo microCT imaging. In light of these data, in vivo microCT imaging represents a valuable tool for investigating bone remolding and has the potential to be used for routine, high-throughput analysis and screening of investigation therapeutics.