An apparatus, program product and method automatically back annotate a functional definition of a circuit design based upon the physical layout generated from the functional definition. A circuit design may be back annotated, for example, by generating a plurality of assignments between a plurality of circuit elements in the circuit design and a plurality of signals defined for the circuit design using a physical definition of the circuit design that has been generated from the functional definition, and modifying the functional definition of the circuit design to incorporate the plurality of assignments into the functional definition.