Many studies show that iron deficient (ID) children are at risk for poor cognitive development. This suggests that learning and cognitive centers in the brain, such as the hippocampus, may be compromised by developmental ID. The present study used a heart rate trace fear conditioning procedure in rats to show that perinatal nutritional ID impairs hippocampus-dependent learning. This procedure requires rats to associate a conditioned stimulus and a fearful unconditioned stimulus, which are separated by a trace interval. Rats were started on ID or control (CN) diets 10 days prior to birth, and learning was assessed on post natal day (PND)-28. The ID pups were impaired in trace fear coniditioning, but an ID control group was not impaired in a non-trace basic fear conditioning procedure that does not depend on the hippocampus. Another group was switched from ID to CN diet on PND-31, and this group also showed impairments in trace fear conditioning when tested during early adulthood (i.e. PND-63). Separate control tests show that ID may produce skeletal motor deficits. The ID-induced learning impairments in this study, however, were not due to altered motor activity because learning was assessed using non-motor heart rate responses.