A comprehensive investigation of antiphase domain boundaries (APB's) in GaAs-on-Si is presented. A comprehensive experimental approach, based on complementary electron microscopy (TEM and SEM) and chemical etch techniques, is developed and used in the study of the structural evolution of APB's on vicinal (001)Si substrates. The question of whether a GaAs selective nucleation or APB annihilation accounts for the absence of APB's in thick GaAs/Si films, grown on substrates misoriented from (001) toward (110), is addressed. APB's are revealed by two different TEM techniques to exist in the first interfacial layers of GaAs/Si even in samples considered to be “APB free”. The APB annihilation mechanism is illustrated in GaAs films grown on substrates misoriented toward (100), either directly, by cross-sectional TEM observations, or indirectly, by combined chemical etch/SEM experiments. In addition, the structural characteristics of APB's and their interaction with other extended crystal defects are clarified by XTEM and TEM observations. Finally, the influence of APB's on GaAs/Si surface morphology and their electrical activity are shown explicitly for the first time.