We obtained perpendicular lamellar orientations in thin films of symmetric polystyrene-block-poly(methyl methacrylate), PS-b-PMMA, on self-assembled monolayers (SAMs) of 3-(p-methoxyphenyl)propyltrichlorosilane (MPTS) prepared on silicon wafers. In contrast to completely parallel lamellae on silicon wafers having a native oxide layer, perpendicular lamellae at the MPTS interface with parallel lamellae at the air interface were directly observed by transmission electron microscopy (TEM) in cross-sectional view. The perpendicular lamellae at the MPTS interface were attributed to the non-preferential (neutral) MPTS-covered substrate to both PS and PMMA blocks. The neutrality of the SAMs of MPTS was confirmed by the similar interfacial tension values of the SAMs of MPTS with PS and PMMA, estimated by contact angle measurements.