A trench capacitor with an isolation collar in a semiconductor substrate where the substrate adjacent to the isolation collar is free of dopants caused by auto-doping. The method of fabricating the trench capacitor includes the steps of forming a trench in the semiconductor substrate; depositing a dielectric layer on a sidewall of the trench; filling the trench with a first layer of undoped polysilicon; etching away the first layer of undoped polysilicon and the dielectric layer from an upper section of the trench whereby the semiconductor substrate is exposed at the sidewall in the upper section of the trench; forming an isolation collar layer on the sidewall in the upper section of the trench; and filling the trench with a second layer of doped polysilicon.