Many physicians, anatomists and natural philosophers engaged in attempts to map the seat of the soul during the so-called Scientific Revolution of the European seventeenth century. The history of these efforts needs to be told in light of the puzzlement bred by today's strides in the neurological sciences. The accounts discussed here, most centrally by Nicolaus Steno, Claude Perrault and Thomas Willis, betray the acknowledgement that a gap remained between observable form, on the one hand, and motor and sensory functions, on the other. Observation yielded information about form, but did not guarantee a constant correlation with presumed function, while the mechanisms of sense and movement did not fit in with accounts of action and cognition whose purpose was to place the connection between active body and willful, conscious soul onto a descriptive rather than metaphysical plane. Teleology was now no longer a helpful tool in the disciplines of anatomy and physiology; the consequences of this are still with us.