The expression of two immediate-early genes (IEGs), Zif268 and c-Fos, was quantified in hippocampal subregions and related structures following spatial learning in the Morris water-maze. A critical feature was the novel control protocol alongside more standard controls, the purpose of which was to test whether hippocampal activity is set automatically when traversing an environment or whether it is dependent on reaching a specific goal using learning that requires the hippocampus (i.e. task dependent). The new control protocol (Procedural Task) made it possible to match swim time, swim distance and learning to escape from water with that of the experimental (Working Memory) group. Unlike the Working Memory group, the Procedural Task animals showed no evidence of learning the absolute platform location during the test session. While the Working Memory rats showed c-Fos increases relative to the Procedural Task controls in the frontal and parahippocampal cortices, hippocampal levels did not differ. Again, for Zif268 there was no evidence of a relative increase of hippocampal activity in the Working Memory group. In fact, hippocampal Zif268 showed evidence of a relative decrease, even though the spatial working memory task is hippocampal dependent. The study not only highlighted the shortcomings of other control procedures used in water-maze studies (free-swimming or home cage control), but also indicated that the expression of these IEGs in the hippocampus is not a direct predictor of explicit spatial location learning. Rather, the activity in combinations of regions, including prefrontal cortex, provides a stronger correlate of water-maze learning.