A method and apparatus to test the inter-die interface between two or more semiconductor die in die stacking applications, where a mismatch exists between the number of input and output pads on a base die and the number of input and output pads on a stacked die. In a first embodiment, a number of through-die vias (TDVs) may be used to implement inter-die signal paths using standard or flexible design rules to maintain statistical TDV yield despite the lack of continuity verification of the inter-die signals paths. In alternate embodiments, programmable multiplexers may be utilized to share one or more inter-die connections between the base die and the one or more stacked die so as to facilitate testing and normal operation of each inter-die connection. In other embodiments, spare TDVs are utilized only during test operations, so as to accommodate the mismatch. In yet other embodiments, built-in-test (BIT) circuits are configured to perform logic operations using a plurality of inter-die input/output (I/O) signals to eliminate the need to implement an identical number of input and output ports between the base die and the one or more stacked die to facilitate inter-die testing.