A high-voltage transistor structure is provided that includes a self-aligned isolation feature between the gate and drain. Normally, the isolation feature is not self-aligned. The self-aligned isolation process can be integrated into standard CMOS process technology. In one example embodiment, the drain of the transistor structure is positioned one pitch away from the active gate, with an intervening dummy gate structure formed between the drain and active gate structure. The dummy gate structure is sacrificial in nature and can be utilized to create a self-aligned isolation recess, wherein the gate spacer effectively provides a template for etching the isolation recess. This self-aligned isolation forming process eliminates a number of the variation and dimensional constraints attendant non-aligned isolation forming techniques, which in turn allows for smaller footprint and tighter alignment so as to reduce device variation. The structure and forming techniques are compatible with both planar and non-planar transistor architectures.