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A great deal of complex cognitive processing occurs at the unconscious level and affects how humans behave, think, and feel. Scientists are only now beginning to understand how this occurs on the neural level. Understanding the neural basis of consciousness requires an account of the neural mechanisms that underlie both conscious and unconscious thought, and their dynamic interaction. For example, how do conscious impulses, thoughts, or desires become unconscious (e.g., repression) or, conversely, how do unconscious impulses, desires, or motives become conscious (e.g., Freudian slips)? Research taking advantage of advances in technologies, like functional magnetic resonance imaging, has led to a revival and re-conceptualization of some of the key concepts of psychoanalytic theory, but steps toward understanding their neural basis have only just commenced. According to psychoanalytic theory, unconscious dynamic processes defensively remove anxiety-provoking thoughts and impulses from consciousness in response to one's conflicting attitudes. The processes that keep unwanted thoughts from entering consciousness include repression, suppression, and dissociation. In this literature review, studies from psychology and cognitive neuroscience in both healthy and patient populations that are beginning to elucidate the neural basis of these phenomena are discussed and organized within a conceptual framework. Further studies in this emerging field at the intersection of psychoanalytic theory and neuroscience are needed.