During development the subthalamus is continuous with the hypothalamus, but is separated by white matter fibres mainly from the internal capsule. Caudally, the subthalamus or prethalamus is separated from the thalamus by the zona limitans intrathalamica. Other nuclei of the subthalamus are the zona incerta, thalamic reticular nucleus, and the fields of Forel.
The subthalamus develops efferent (output) connections to the striatum (caudate nucleus and putamen) in the telencephalon, to the dorsal thalamus (medial and lateral nuclear groups) in the diencephalon, and to the red nucleus and substantia nigra in the mesencephalon. It receives afferent (input) connections from the substantia nigra and striatum.