Within substance abuse, neuroimaging has experienced tremendous growth as both a research method and a clinical tool in the last decade. The application of functional imaging methods to cocaine dependent patients and individuals in treatment programs, has revealed that the effects of cocaine are not limited to dopamine-rich subcortical structures, but that the cortical projection areas are also disrupted in cocaine dependent patients. In this review, we will first describe several of the imaging methods that are actively being used to address functional and structural abnormalities in addiction. This will be followed by an overview of the cortical and subcortical brain regions that are most often cited as dysfunctional in cocaine users. We will also introduce functional connectivity analyses currently being used to investigate interactions between these cortical and subcortical areas in cocaine users and abstainers. Finally, this review will address recent research which demonstrates that alterations in the functional connectivity in cocaine users may be associated with structural pathology in these circuits, as demonstrated through diffusion tensor imaging. Through the use of these tools in both a basic science setting and as applied to treatment seeking individuals, we now have a greater understanding of the complex cortical and subcortical networks which contribute to the stages of initial craving, dependence, abstinence, and relapse. Although the ability to use neuroimaging to predict treatment response or identify vulnerable populations is still in its infancy, the next decade holds tremendous promise for using neuroimaging to tailor either behavioral or pharmacologic treatment interventions to the individual.