Surface-initiated atom transfer radical polymerization of 2-(perfluorooctyl)ethyl acrylate on a flat silicon wafer was carried out to give poly {2-(perfluorooctyl)ethyl acrylate} (PFA-C-8) brush thin film with three different thicknesses of 4, 11, and 43 nm, respectively. The water contact angle of the PFA-C-8 brush surface was 120 degrees. The molecular aggregation state of the perfluoroalkyl (R-f) group of PFA-C-8 brush was analyzed by X-ray reflectivity (XR), wide-angle X-ray diffraction, and grazing incidence X-ray diffraction (GIXD) measurements. XR analysis revealed that Rf groups at the air/brush interface formed a densely packed structure, while a relatively low-density region was generated at the brush/substrate interface. The peaks of in-plane GIXD for brush films with thicknesses of 11 and 43 nm were observed at q(xy) = 12.5 nm(-1), which indicated that Rf groups at the outermost surface oriented perpendicular to the surface of silicon substrate. In an out-of-plane diffraction profile of the 43 nm-thick PFA-C-8 brush film, peaks corresponding to a periodic length of the bilayer lamellae were observed. Therefore, R-f groups of the thicker brush film were crystallized and formed ordered bilayer lamellar structure at the outermost surface. In contrast, no diffraction pattern was observed from the PFA-C-8 at a thickness of 4 nm by WAXD and GIXD. These results indicate that an amorphous layer was formed at the interface of the brush/substrate. The Rf groups at the anchoring region of the brush could not form a sufficiently ordered structure due to immobilization of brush chain ends on the substrate. It was suggested that the R-f groups in a PFA-C-8 brush thin film at the Outermost Surface aggregated in a different manner from those in the anchoring region.