In this paper we focus on the understanding of the morphological behaviour of Polyamide 66 (PA66) in a constrained geometry generated by adsorption onto chemically controlled interfaces such as thiol self-assembled monolayers (SAMs) grafted on gold substrates. The latter are prepared under different experimental conditions to illustrate the mechanism of PA-SAM interaction. The crystalline morphology of polyamide nanofilms, analysed by atomic force microscopy, was found to be dependent directly on the surface chemistry that is controlled by the thiol functionality (e.g. NH2- and COOH- terminated thiols) and by the density and the structural organization of the grafts. These two parameters depend on the immersion times of the gold substrate in the thiol solutions. Furthermore, a direct correlation is evidenced between the polyamide morphology in thin films and its crystalline amount, as calculated by polarization-modulation infrared reflection-absorption spectroscopy. Quantitative results propose an interfacial interaction mechanism between the polyamide chains and the surface grafts, and give information about the SAM formation kinetics and its organization during the grafting process. Copyright (C) 2003 John Wiley Sons, Ltd.