Through-silicon vias (TSVs), being one of the key enabling technologies for 3D system integration, are being used in various 3D vertically stacked devices. As TSVs are relatively new, there is not enough information in available literature on the thermo-mechanical reliability of TSVs. Due to the high coefficient of thermal expansion (CTE) mismatch between Si and the Cu vias, “Cu pumping” will occur at high temperature and “Cu sinking” will occur at low temperature, which may induce large stress in SiO2, interfacial stress at Cu/SiO2 interface and plastic deformation in Cu core. The thermal-mechanical stress can potentially cause interfacial debonding, cohesive cracking in dielectric layers or Cu core, causing some reliability issues. Thus, in this paper, three-dimensional thermo-mechanical finite-element models have been built to analyze the stress/strain distribution in the TSV structures. A comparative analysis of different via designs, such as circular, square, and annular vias has been performed. In addition, defects due to fabrication such as voids in the Cu core during electroplating and Cu pad undercutting due to over-etching are considered in the models, and it is seen that these fabrication defects are detrimental to TSV reliability.