A three-dimensional integrated circuit comprising top tier nanowire transistors formed on a bottom tier of CMOS transistors, with inter-tier vias, intra-tier vias, and metal layers to connect together the various CMOS transistors and nanowire transistors. The top tier first begins as lightly doped regions on a first wafer, with an oxide layer formed over the regions. Hydrogen ion implantation forms a cleavage interface. The first wafer is flipped and oxide bonded to a second wafer having CMOS devices, and the cleavage interface is thermally activated so that a portion of the lightly doped regions remains bonded to the bottom tier. Nanowire transistors are formed in the top tier layer. The sources and drains for the top tier nanowire transistors are formed by in-situ doping during epitaxial growth. After oxide bonding, the remaining process steps are performed at low temperatures so as not to damage the metal interconnects.