C.G. Jung’s theory of psychological complexes lies at the root of analytical psychology theory and practice. Functional magnetic resonance imaging (fMRI) provides a powerful tool to validate the theory of complexes and eludicate the neuropsychologic mechanisms underlying the unconscious activation of significant memories. In this study, using fMRI, we identify two brain circuits which are activated in response to complex triggering words. Circuit one involves brain regions involved in episodic memory and somatic (body) responses and the experience of uncertainty. A second circuit involves episodic memory, emotion, visual and language association, and semiotic meaning. Specific brain regions include the right prefrontal cortex, SMA cortex, left temporal cortex, and the caudate and cingulate. These brain circuits may be thought of as the biological form in which complexes are experienced. Implications for analytic psychology practice and theory are discussed.