We present the study of poly(2-methoxyaniline) and poly(2,5-dimethoxyaniline) chemical deposition in situ on gold electrodes coated with self-assembled thiol monolayers (SAM) containing different terminal groups: methyl, hydroxy, and carboxy. The differences in the deposition rates of polymers on various thiol monolayers were investigated with the quartz crystal microbalance (QCM) and UV-Vis spectroscopy. It was found that for poly(2,5-dimethoxyaniline) the polymer is formed in the bulk of the polymerisation solution and subsequently or simultaneously it accumulates on the substrate surface. The data obtained for poly(2-methoxyaniline) suggest substantially different mechanism of deposition. The polymerisation is initiated on SAM-modified gold, and this process is strongly influenced by the chemical nature of the monolayer. Thus, we observed large differences in the deposition rates on 'hydrophobic' and 'hydrophilic' monolayers modifying the electrode surface. The effect of the underlying thiol monolayer on the morphology of synthesised polymers was also investigated by atomic force microscopy (AFM).