Poly(dimethylsiloxane) (PDMS) is the most widely used stamp material in microcontact printing. It has excellent properties with respect to versatility, chemical inertness, and mechanical stability. However, it has an inclination to contaminate printed substrates with low molecular weight siloxane fragments. In this study, it is shown, by a combination of lateral force microscopy, Fourier transform infrared spectroscopy, and X-ray photoelectron spectroscopy, that the extent of the PDMS-induced contamination is dependent on the nature of the ink used. The highest degree of contamination was found for relatively polar inks, whereas apolar alkanethiol inks were found to shield the substrate from contamination. This is interpreted in terms of the contaminating species being polar in nature.