Microcontact printing (μCP) is a widely used method to make miniaturized patterns on surfaces. In this work, the issue of the possible transfer of stamp material from the stamp to the substrate during stamping was addressed. Poly(dimethylsiloxane) was used to stamp Milli-Q water or buffer on substrates of SiOx, TiO2, and Au. X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to measure and characterize the substrate before and after stamping to detect the possible transfer of stamp-related material to the substrates. Both the XPS and the ToF-SIMS analyses show that silicone-related material is transferred from flat stamps and that even more material is transferred from patterned stamps. Interestingly, a UV/ozone treatment (essentially oxidation of the surface) of the stamps before inking and stamping significantly reduces the silicone transfer. Two application examples are used to illustrate the importance of silicone transfer to the substrates during μCP: water condensation patterns and supported lipid bilayer formation.