Sub-micron layers of poly(3-octylthiophene) and poly(3-hexylthiophene) deposited by spin-casting on glass substrates were for the first time investigated by X-ray diffraction using synchrotron radiation. The polymers have a partial crystalline structure and are, in contrast to bulk materials, oriented with their side chains parallel to the substrate surface. Optical absorption spectra obtained from the same samples show that the conjugation length is related to the crystalline order.