Skybridges and atria between buildings are becoming more and more popular. Most current skybridge connections are either roller or rigid-connections. This dissertation presents an investigation of the structural analysis and optimization of skyscraper systems with hinge-connected skybridges, and compares the results to skyscraper systems with roller-connected skybridges and to skyscraper systems without skybridges altogether. Also presented is an investigation of the structural analysis and optimization of skyscrapers both with and without atria between the buildings. It was assumed that the atria envelope was constructed with cushions made from lightweight, transparent, and flexible Ethylene Tetrafluoroethylene (ETFE). A simplified skyscraper skybridge model (SSSM) was developed to approximate analysis of such systems. The SSSM identifies and includes only the dominant degrees of freedom (DOF's) when assembling the structure stiffness matrix. This greatly reduces computational time and computer memory compared to traditional finite element models (FEM). The SSSM is fast enough to be used with both gradient-based and genetic optimization algorithms. The steps of the SSSM consist of: 1) determination of megacolumn areas, 2) constructing the stiffness matrix, 3) evaluation of volume, weight, mass and period, 4) calculation of lateral force vectors, and 5) calculation of displacement and stress constraints. Three skyscraper systems were analyzed using both the SSSM and a FEM to compare both the accuracy and efficiency of the SSSM. It was found that the SSSM was very accurate for displacements (translations and rotations), and core, megacolumn, outrigger, and skybridge stress. It was also found that the SSSM analysis time was significantly faster and used far less computer memory than FEM. Four skyscraper systems were optimized for two different sites, with varying atria and skybridge conditions, using gradient-based and genetic optimization algorithms. The optimization strategy consisted of a series of executions of the sequential quadratic programming (SQP) algorithm, followed by executions of the generalized reduced gradient (GRG) algorithm, followed by executions of a discrete genetic algorithm. The genetic algorithm made significant progress for two of the systems. Optimal results showed that in some cases hinge skybridges and atria envelope produced significantly lighter systems compared to roller, no skybridge, or without atria envelope cases.