Bioactive glasses are a class of synthetic inorganic material that have wide orthopedics, dentistry, tissue engineering and other biomedical applications. The origin of the bioactivity is closely related to the atomic structures of these novel glass materials, which otherwise lack long range order and defies any direct experimental measurements due to their amorphous nature. The structure of bioactive glasses is thus essential for the understanding of bioactive behaviors and eventually rational design of glass compositions. In this dissertation, molecular dynamics (MD) and reverse monte carlo (RMC) based computer simulations have been used to systematically study the atomic structure of three classes of new bioactive glasses: strontium doped 45S5 Bioglass®, ZnO-SrO containing bioactive glasses, and Cao-MgO-P2O5-SiO2 bioactive glasses. Properties such as ionic diffusion that are important to glass dissolution behaviors are also examined as a function of glass compositions. The accuracy of structure model generated by simulation was validated by comparing with various experimental measurements including X-ray/neutron diffraction, NMR and Raman spectroscopy. It is shown in this dissertation that atomistic computer simulations, when integrated with structural and property characterizations, is an effective tool in understanding the structural origin of bioactivity and other properties of amorphous bioactive materials that can lead to design of novel materials for biomedical applications.