Patterned self-assembled monolayers have been fabricated by the reductive desorption of mercaptoacetic acid in mixed monolayers of mercaptoacetic acid and C16SH in alkaline solution. The greater the content of C16SH in the monolayers, the more negative is the reductive desorption potential of mercaptoacetic acid, indicating that mercaptoacetic acid and C16SH did not form patched domains, but mixed well with each other. The electrochemical deposition of pyrrole has been investigated at the patterned monolayers by cyclic voltammetry and atomic force microscopy (AFM). The results show that the polymer film growth strongly depends on the integrity of such patterned monolayers. In the case of patterned monolayers of high integrity, the polypyrrole grows on the top of the monolayers. However, in the case of a large number of pinhole defects, the polymerization results in the formation of polymer nuclei on pinhole sites scattered in the insulating monolayer matrix. The nuclei act as conducting paths to make the redox of the electroactive species more facile.