In organic field effect transistors, charge transport is confined to a narrow region next to the organic/dielectric interface. It is thus extremely important to determine the morphology and the molecular arrangement of the organic films at their early growth stages. On a substrate of technological interest, such as thermally grown silicon oxide, it has been recently found that R-sexithienyl aggregates made of flat-lying molecules can simultaneously nucleate besides islands made of molecules standing vertical. In this paper, we investigate the effects due to variations in surface chemical composition on R-sexithienyl ultrathin film formation. Flatlying molecules are no longer detected when Si-OH groups present at the surface are chemically removed but also when the Si-OH or Si-H group density is maximized. This gives evidence that variations in the surface chemical composition can largely affect the nucleation and growth processes of organic/dielectric interfaces. We hypothesize that isolated OH groups can interact with R-sexithienyl molecules and anchor them down flat with respect to the surface.