This paper introduces a new three-dimensional analysis of complex disordered porous media. Skeleton graph analysis is described and applied to trabecular bone images obtained by high resolution magnetic resonance imaging. This technique was developed bearing in mind topological considerations. The correspondence between vertices and branches of the skeleton graph and trabeculae is used in order to get local information on trabecular bone microarchitecture. In addition to real topological parameters, local structural information about trabeculae, such as length and volume distributions, are obtained. This method is applied to two sets of samples: six osteoporosis and six osteoarthritis bone samples. We demonstrate that skeleton graph analysis is a powerful technique to describe trabecular bone microarchitecture.