Articular stress fracture arising from the distal end of the third metacarpal bone (MC3) is a common serious injury in Thoroughbred racehorses. Currently, there is no method for predicting fracture risk clinically. We describe an ex-vivo biomechanical model in which we measured subchondral crack micromotion under compressive loading that modeled high speed running. Using this model, we determined the relationship between subchondral crack dimensions measured using computed tomography (CT) and crack micromotion. Thoracic limbs from 40 Thoroughbred racehorses that had sustained a catastrophic injury were studied. Limbs were radiographed and examined using CT. Parasagittal subchondral fatigue crack dimensions were measured on CT images using image analysis software. MC3 bones with fatigue cracks were tested using five cycles of compressive loading at -7,500N (38 condyles, 18 horses). Crack motion was recorded using an extensometer. Mechanical testing was validated using bones with 3 mm and 5 mm deep parasagittal subchondral slots that modeled naturally occurring fatigue cracks. After testing, subchondral crack density was determined histologically. Creation of parasagittal subchondral slots induced significant micromotion during loading (p<0.001). In our biomechanical model, we found a significant positive correlation between extensometer micromotion and parasagittal crack area derived from reconstructed CT images (SR = 0.32, p<0.05). Correlations with transverse and frontal plane crack lengths were not significant. Histologic fatigue damage was not significantly correlated with crack dimensions determined by CT or extensometer micromotion. Bones with parasagittal crack area measurements above 30 mm2 may have a high risk of crack propagation and condylar fracture in vivo because of crack micromotion. In conclusion, our results suggest that CT could be used to quantify subchondral fatigue crack dimensions in racing Thoroughbred horses in-vivo to assess risk of condylar fracture. Horses with parasagittal crack arrays that exceed 30 mm2 may have a high risk for development of condylar fracture.