Self-assembled monolayers (SAMs) of dodecanethiol on gold formed by solution assembly and microcontact printing were compared using electron spectroscopy for chemical analysis (ESCA) and time-of-flight secondary ion mass spectrometry (SIMS). Both univariate (ESCA and TOF-SIMS) and multivariate (TOF-SIMS) analysis techniques were employed. Univariate analysis showed that samples stamped with a thiol concentration > 10-50 mM produced SAMs comparable to long solution assembly times. Principal component analysis (PCA) of the SIMS spectra provided deeper insight into the two sets of samples. The scores from the first principal component (PC1) showed similarities between the samples prepared by the two methods, though there was more scatter in the microcontact printed samples. The second principal component (PC2) showed that differences exist between the solution assembled and stamped samples due mainly to a relative increase in the presence of oxidized species (SO3-, HSO4-, O-, OH-, (M-H)(oxidized)(-)) and silicone contaminants on the stamped samples. This is in contrast to the univariate data that showed only random trace amounts of Si (< 1%) by ESCA analysis on a few spots sampled. Information from this study was used to suggest ways of minimizing surface contamination in microcontact printing of thiols. We suggest extensive precleaning of the stamp and use of higher thiol ink concentrations (at least 10-50 mM).