A method and apparatus for programming anti-fuses using a positive voltage switching circuit for connecting an external terminal receiving a positive programming voltage to one plate of an anti-fuse responsive to an active program enable signal. A negative voltage switching circuit connects an external terminal receiving a negative programming voltage to the other plate of the anti-fuse responsive to the active program enable signal. The negative voltage switching circuit normally maintains one plate of the anti-fuse at ground potential when the anti-fuse is not being programmed so that its conductive state can be read by applying a voltage to the other plate of the anti-fuse. The transistors used in the negative voltage switching circuit are fabricated in a well that is isolated from the substrate in which the transistors in the positive voltage switching circuit are fabricated. As a result, the negative programming voltage coupled to the well is not coupled to the substrate, thereby avoiding overstress of the gate oxide layers and p-n junctions in MOSFETs of the integrated circuit. The negative voltage switching circuit includes a switch for coupling the well and the substrate to each other during normal operating modes and for isolating them from each other when the anti-fuse is being programmed.