The key issue in analyzing brain substrates of memory is the nature of memory traces, how memories are formed, stored, and retrieved in the brain. In order to analyze mechanisms of memory formation it is first necessary to find the loci of memory storage, the classic problem of localization. Various approaches to this issue are reviewed. A particular strategy is proposed that involves a number of different techniques (electrophysiological recording, lesions, electrical stimulation, pathway tracing) to identify the essential memory trace circuit for a given form of learning and memory. The methods of reversible inactivation can be used to localize the memory traces within this circuit. Using classical conditioning of eye blink and other discrete responses as a model system, the essential memory trace circuit is identified, the basic memory trace is localized (to the cerebellum), and putative higher-order memory traces are characterized in the hippocampus.