The introduction of finite element analysis (FEA) into orthopaedic biomechanics allowed continuum structural analysis of bone and bone-implant composites of complicated shapes (Huiskes and Chao, J. Biomechanics, Vol. 16, 1983, pp. 385–409). However, besides having complicated shapes, musculoskeletal tissues are hierarchical composites with multiple structural levels that adapt to their mechanical environment. Mechanical adaptation influences the success of many orthopaedic treatments, especiallly total joint replacements. Recent advances in FEA applications have begun to address questions concerning the optimality of bone structure, the processes of bone remodeling, the mechanics of soft hydrated tissues, and the mechanics of tissues down to the microstructural and cell levels. Advances in each of these areas, which have brought FEA from a continuum stress analysis tool to a tool which plays an ever-increasing role in the scientific understanding of tissue structure, adaptation, and the optimal design of orthopaedic implants, are reviewed.