We investigate the effect of confinement on the crystalline microstructure of the polymer component of polymer : fullerene bulk heterojunction thin films using grazing incidence wide angle X-ray scattering. We find that the polymer crystallite size decreases and the alignment of the molecules along the surface normal increases, as the thin-film thickness is reduced from 920 nm to <20 nm and approaches the thin-film confinement regime. Furthermore, we find that the polymer crystallite size near the surface (air interface) is lower than the crystallite size in the bulk or the bottom (substrate interface) of bulk heterojunction films thicker than the confinement regime. Variation in polymer crystallite size can cause changes in charge carrier mobility and recombination rates, which in turn affect the performance of bulk heterojunction thin film devices such as photovoltaics and photodetectors.