The objective of this study was to provide an overarching description of the inter-subject variability of the equine femur and tibia morphology using statistical shape modeling. Fifteen femora and fourteen tibiae were used for building the femur and tibia statistical shape models, respectively. Geometric variations in each mode were explained by biometrics measured on ±3 standard deviation instances generated by the shape models. Approximately 95% of shape variations within the population were described by 6 and 3 modes in the femur and tibia shape models, respectively. In the femur shape model, the first mode of variation was scaling, followed by notable variation in the femoral mechanical-anatomical angle and femoral neck angle in mode 2. Orientation of the femoral trochlear tubercle and femoral version angle were described in mode 3 and mode 4, respectively. In the tibia shape model, the main mode of variation was also scaling. In mode 2 and mode 3, the angles of the coronal tibial plateau and the medial and lateral caudal tibial slope were described, showing the lateral caudal tibial slope angle being significantly larger than the medial. The presented femur and tibia shape models with quantified biometrics, such as femoral version angle and posterior tibial slope, could serve as a baseline for future investigations on correlation between the equine stifle morphology and joint disorders due to altered biomechanics, as well as facilitate the development of novel surgical treatment and implant design. By generating instances matching patient-specific femorotibial joint anatomy with radiographs, the shape model could assist virtual surgical planning and provide clinicians with opportunities to practice on 3D printed models.