Methods, structure and design structure having isolated back gates for fully depleted semiconductor-on-insulator (FDSOI) devices are presented. In one embodiment, a method may include providing a FDSOI substrate having a SOI layer over a buried insulator over a first polarity-type substrate, the first polarity-type substrate including a second polarity-type well therein of opposite polarity than the first polarity; forming a trench structure in the FDSOI substrate; forming an active region to each side of the trench structure in the SOI layer; and forming a PFET on the active region on one side of the trench structure and an NFET on the active region on the other side of the trench structure.