A novel method for the electrochemical dissolution of polyelectrolyte multilayers from the surface of an electrode for applications in controlled drug delivery is reported. Biodegradable and biocompatible multilayer films based on poly(L-lysine) and heparin have been selected as a model system, and have been built on an indium tin oxide semiconductor substrate. The build-up and dissolution processes of the multilayers is followed by electrochemical optical waveguide light mode spectroscopy. The formation and stability of the polyelectrolyte multilayers have been found to depend on the applied potential and the ionic strength of the buffer. The application of potentials above a threshold of 1.8 V induces dissolution, which follows single-exponential kinetics, of the polyelectrolyte multilayer film. The rate of this process can be varied by an on–off profile of the potential, leading to the controlled release of heparin into the bulk. Atomic force microscopy investigations show that the electrodissolution of the polyelectrolyte multilayers is a local phenomenon that leads to the formation of nanoporous films.