Traditional methods of drug discovery often rely on a unidirectional, "bottom-up" approach: A search for molecular compounds that target a particular neurobiological substrate (e.g., a receptor type), the refinement of those compounds, testing in animal models using high-throughput behavioral screening methods, and then human testing for safety and effectiveness. Many attempts have found the "effectiveness" criterion to be a major stumbling block, and we and others have suggested that success may be improved by an alternative approach that considers the neural circuits mediating the effects of genetic and molecular manipulations on behavior and cognition. We describe our efforts to understand the cholinergic system's role in attention using parallel approaches to test main hypotheses in both rodents and humans as well as generating converging evidence using methods and levels of analysis tailored to each species. The close back-and-forth between these methods has enhanced our understanding of the cholinergic system's role in attention both "bottom-up" and "top-down"-that is, the basic neuroscience identifies potential neuronal circuit-based mechanisms of clinical symptoms, and the patient and genetic populations serve as natural experiments to test and refine hypotheses about its contribution to specific processes. Together, these studies have identified (at least) two major and potentially independent contributions of the cholinergic system to attention: a neuromodulatory component that influences cognitive control in response to challenges from distractors that either make detection more difficult or draw attention away from the distractor, and a phasic or transient cholinergic signal that instigates a shift from ongoing behavior and the activation of cue-associated response. Right prefrontal cortex appears to play a particularly important role in the neuromodulatory component integrating motivational and cognitive influences for top-down control across populations, whereas the transient cholinergic signal involves orbitofrontal regions associated with shifts between internal and external attention. Understanding how these two modes of cholinergic function interact and are perturbed in schizophrenia will be an important prerequisite for developing effective treatments.