Researchers often attribute higher cognition to the enlargement of cortical regions throughout evolution, reflecting the belief that humans sit at the top of the cognitive pyramid. Implicitly, this approach assumes that the subcortex is of secondary importance for higher-order cognition. While it is now recognized that subcortical regions can be involved in various cognitive domains, it remains unclear how they contribute to computations essential for higher-level cognitive processes such as endogenous attention and numerical cognition. Herein, we identify three models of subcortical–cortical relations in these cognitive processes: (i) subcortical regions are not involved in higher cognition; (ii) subcortical computations support elemental forms of higher cognition mainly in species without a developed cortex; and (iii) higher cognition depends on a whole-brain dynamic network, requiring integrated cortical and subcortical computations. Based on evolutionary theories and recent data, we propose theSEED hypothesis: the Subcortex is Essential for the Early Development of higher cognition. According to the five principles of theSEED hypothesis, subcortical computations are essential for the emergence of cognitive abilities that enable organisms to adapt to an ever-changing environment. We examine the implications of theSEED hypothesisfrom a multidisciplinary perspective to understand how the subcortex contributes to various forms of higher cognition.