The production of reproducible self-assembled monolayers (SAMs) is essential to many nano(bio)-technology applications. To check the effects of different cleaning methods on a reproducible SAMs formation, the cleaning methods were varied and then used for preparing each SAM. The reproducibility of each SAM was examined by ToF-SIMS analysis along with principal component analysis (PCA). Using what we found to be a superior method of cleaning gold surfaces, alkanethiol SAMs with different terminal groups such as 1-dodecanethiol (DDT), 11-mercaptoundecanoic acid (MUA), 11-mercapto-1-undecanol (MUD) were reproduced. Our statistical results show that reproducible alkanethiol SAMs on a well-cleaned gold surface can be produced within only a few standard deviation percentages obtained from point-to-point and sample-to-sample spectra. (C) 2008 Elsevier B. V. All rights reserved.