Three-dimensional statistical shape models built from MRI data can predict future disease and distinguish between groups. However, these models do not leverage the major advantage of MRI – the ability to visualize and quantify soft tissues such as cartilage. This study built three MRI-based statistical shape models, 1) bone shape, 2) cartilage thickness, 3) both bone shape and cartilage thickness. We showed that bone shape and bone shape + cartilage thickness models predicted sex with an R2 of ~0.9, significantly outperforming cartilage thickness alone (0.8). However, cartilage thickness alone was significantly better at predicting radiographic knee osteoarthritis.