We consider the task of computing shape statistics and classification of 3D anatomical structures (as continuous, parameterized surfaces) under a Riemannian framework. This task requires a Riemannian metric that allows: (1) reparameterizations of surfaces by isometries, and (2) efficient computations of geodesic paths between surfaces. These tools allow for computing Karcher means and covariances (using tangent PCA) for shape classes, and a probabilistic classification of surfaces into disease and control classes. In a separate paper [13], we introduced a mathematical representation of surfaces, called q-maps, and we used the L2 metric on the space of q-maps to induce a Riemannian metric on the space of parameterized surfaces. We also developed a path-straightening algorithm for computing geodesic paths [14]. This process requires optimal reparameterizations (deformations of grids) of surfaces and achieves a superior alignment of geometric features across surfaces. The resulting means and covariances are better representatives of the original data and lead to parsimonious shape models. These two moments specify a normal probability model on shape classes, which are then used for classifying test shapes. Through improved random sampling and a higher classification performance, we demonstrate the success of this model over some past methods. In addition to toy objects, we use the Detroit Fetal Alcohol and Drug Exposure Cohort data to study brain structures and present classification results for the Attention Deficit Hyperactivity Disorder cases and controls in this study.We find that using the mean and covariance structure of the given data, we are able to attain a 88% classification rate, which is an improvement over a previously reported result of 82% on the same data