There has always been confusion and disagreement about the nature of the terms archetype and complex in Jungian circles, not to mention non-Jungian ones. Another ongoing concern is whether Jung's concept of the archetype and complex can be justified in terms of current scientific research, most notably that of neurophysiologists and others interested in the brain and consciousness. This paper proposes a theory of the formation of complexes, namely, that they are created through self-organization within the brain/mind. Self-organization is a process typical of large complex systems, and is generally accepted to operate within the brain and to be important in its functioning. Examples of self-organization in biology are related to the psychic processes that form the complexes. It is then natural to define the archetype in terms of the complex, and the authors propose a definition of the archetype as an equivalence class of complexes. On this view, the archetype is an emergent property of the activity of the brain/mind, and is, appropriately, defined at the level at which it emerges. This definition is in line with the original development of Jung's ideas, in that he derived the concept of the archetype from his earlier discovery of the feeling-toned complex.