In recent years, there has been increasing interest in studies of brain plasticity. Although still loosely defined, this term describes the ability of the brain to change. Cortical plasticity encompasses a wide variety of phenomena and mechanisms, including modifications in cortical properties such as strength of internal connections, representational patterns, or neuronal modifications, either morphological or functional (Donoghue et al., 1996). We focus on the description of different ways in which transcranial magnetic stimulation (TMS) can be used to study patterns of reorganization and some of the mechanisms involved in these changes. Correlation between TMS and neuroimaging studies in humans and animal studies addressing similar questions is discussed. It is important to identify in each situation whether plasticity plays a beneficial role or is maladaptive in terms of functional compensation. The understanding of patterns, mechanisms, and functional relevance of cortical plasticity will hopefully lead to the design of effective strategies to enhance plasticity when it is beneficial and to down-regulate it when it is maladaptive. An example of a possible strategy, using TMS, is discussed.