Neurons in this nucleus give rise to the bulk of efferents from the septal nuclei.

A major projection from the medial septal nucleus terminates in the hippocampal formation.

[2] Specifically, the GABAergic cells of the medial septum that act as theta pacemakers target dentate gyrus, CA3, and CA1 interneurons.

In addition to the theta wave generation, it has recently been discovered that medial septum also serves as an important node for sensory valence processing.

For example, Vglut2 neurons in medial septum respond strongly to noxious sensory stimulation.