Transcranial magnetic stimulation (TMS) is a non-invasive method where an externally placed, rapidly changing magnetic field causes induction of weak electric currents that lead to changes in neuronal polarization and activity. TMS is a modality that has emerged as a unique tool in the study of functional neuroscience for several reasons. TMS can be used to selectively activate or inhibit specific cortical structures, leading to transient perturbations in their function. Systematic study of these perturbations has been employed to determine the function of specific cortical structures and to investigate structure-function relationships. These studies extend to the functional mapping of brain structures as well as brain networks. While TMS was first validated in studies of motor cortex function, it has been applied to the study of cognition and cognitive processing. "Virtual lesions" can be transiently induced in areas of eloquent cortex that allow for the evaluation of their function in cognition and behavior and can be used to evaluate the modes and hierarchy of control of these functions. When TMS is delivered in a repetitive fashion, long-term alterations of cortical function are induced which can be used to study functional brain plasticity, and the changes in brain plasticity in different cognitive states, including aging and diseases involving cognition. Furthermore, repetitive TMS strategies have been developed as possible modulators of cognitive function, with potential to serve as cognitive enhancers in both healthy and disease states. In this review, specific attention is given to the use of TMS in the evaluation of neurophysiologic changes in Alzheimer's disease (AD), as well as the potential role of TMS as a cognitive enhancing therapy in AD.