This contribution reports on the influence of acids oil the quality of carboxylic-acid-terminated self-assembled monolayers (SAMs) on gold prepared from ethanolic solution of HS-(CH2)(15)-COOH and HS-(CH2)(11)CONH-(EG)(6)CH2-COOH. Null ellipsometry, contact angle goniometry, and infrared reflection-absorption spectroscopy are used to monitor the physical and chemical changes occurring within the SAMs upon acid post treatment; after incubation with acids present in the solution: and after incubation in aged acid containing solutions. The presence of acid has a positive effect oil the crystallinity, packing, and orientation Of the Supporting alkyl and ethylene glycol Subunits of the SAM. Our Studies also confirm previous findings stating that the carboxylic groups are rapidly converted into ethyl ester groups in the presence of hydrochloric acid in the incubation solution. It is also evident that the conversion occurs in the presence of the weaker acid, acetic acid, although at a much slower rate than that for hydrochloric acid. This is a new observation that has not been reported on before. The physical and chemical characterization is also complemented with a functional bioaffinity study. The functional evaluation revealed that the present model system was surprisingly insensitive to the degree of esterification of the carboxylic acid groups, but that 4 weeks of storage of the two investigated thiols in hydrochloric acid containing ethanol resulted in SAMs that were completely inactive with respect to immobilization and subsequent binding of the antigen. It was encouraging to note that the nonspecific binding of both antigen and antibody was extremely low oil the two SAMs, regardless of the relative amount of ethyl esters on the surface.