We report on an atomic force microscopy study of polyelectrolyte films of poly(ethyleneimine) (PEI), poly(ethylene-co-maleic acid) (PMAE) and poly(styrene sulfonic acid) sodium salt (PSS) deposited by the layer-by-layer electrostatic technique. The organic thin films were prepared either following self-assembly in a beaker or in a cell with a continuous flow of the polyelectrolyte solutions. Multilayer structures based on PEI/PMAE bilayers are shown to possess much rougher surfaces than those built-up using PEI/PSS bilayers. This is attributed to the strong polyelectrolyte character of PSS. The deposition method is also shown to influence the morphology of the deposited film. Generally, layers built-up in a flow cell were less uniform than those assembled in a beaker. (c) 2005 Elsevier B.V All rights reserved.