COOH-terminated organic surfaces were prepared by self-assembly of different organothiols, mercaptohexadecanoic acid (MHDA) and mercaptomethylterphenylcarboxylic acid (MMTA), on An substrates. The SAMs were explored by infrared reflection-absorption spectroscopy and X-ray photoelectron spectroscopy. A rather strong dependence on preparation conditions is observed which explains inconsistencies between previous studies reported for these systems. Using optimized preparation conditions, films with a high degree of molecular orientation could be prepared. A significant amount of disorder, however, is induced by hydrogen bonds between the terminating -COOH groups. An organothiol with a more rigid backbone, MMTA, is demonstrated to yield carboxy-terminated SAMs which are more straightforward to prepare and which show a significantly higher degree of order.