Methods and structures formed thereby are described, of forming self-aligned contact structures for microelectronic devices. An embodiment includes forming a trench in a source/drain region of a transistor device disposed in a device layer, wherein the device layer is on a substrate, forming a fill material in the trench, forming a source/drain material on the fill material, forming a first source/drain contact on a first side of the source/drain material, and then forming a second source drain contact on a second side of the source/drain material.