A century of behavioral and neurobiological research suggests that Pavlovian conditioning involves three component memory systems: sensorimotor, affective and cognitive. In classical eyeblink conditioning, there is evidence that these three memory systems involve, respectively, the cerebellum, amygdala and hippocampus. This article reviews developmental research on eyeblink conditioning in rodents that is beginning to characterize ontogenetic dissociations and interactions among these memory systems. This research shows that the functional development of the affective system (conditioned fear response) precedes that of the sensorimotor system (conditioned eyeblink reflex). Modulation of these two systems by cognitive processes also seems to emerge at different points in ontogeny. Implications for cognitive development and research on multiple memory systems are discussed.