Agrobacterium-mediated genetic transformation is a process by which the bacterium delivers a specific DNA molecule into plant cells. The transferred DNA molecule (T-DNA) stably integrates into the host genome and is expressed there. Agrobacterium-mediated genetic transformation is widely used for the production of transgenic plants useful for basic plant research and biotechnology, yet the mechanisms by which the T-DNA integrates into the host genome are still poorly understood. Furthermore, we have only recently begun to reveal the important functions of plant factors in the integration process. In this chapter, we describe the current knowledge on the bacterial and host factors and the cellular mechanisms that govern the integration of T-DNA molecules into plant cells. We follow the long line of genetic, functional, and biochemical studies which have paved the way for establishing the different integration models, and we describe possibilities for controlling the T-DNA integration process in order to achieve the most desirable gene-targeting technology for plant species.