Neural processes underlying memory and learning should be studied under the best possible physiological conditions - namely, in alert behaving animals. The classical conditioning of the nictitating membrane and eyelid response is a widely used experimental model for studying the neural bases of motor learning in mammals. Nevertheless, information is still needed on the functional aspects, taking place simultaneously in different cerebral structures, that underlie acquisition, extinction and recall of new motor and cognitive abilities. Here, we review recent data on the neural activity generated in selected brain sites (facial motor nuclei, deep cerebellar nuclei and the hippocampus) in simultaneity with the process of learning. The use of modern technologies for the proper recording of eyelid movements, for the identification of the recorded units, and for the activation of selective synaptic processes during the learning situation enables a precise redefinition of the role played by these neural structures in such associative learning. This review is part of the TINS special issue on The Neural Substrates of Cognition.