Radially polarized ultrafast laser beams are used in the fabrication of three-dimensional photonic crystals with the two-photon polymerization technique in organic-inorganic hybrid materials. It has been found that when a radially polarized beam is employed, the lateral size of the fabricated polymer rods is decreased by 27.5% from 138 to 100 nm under a threshold fabrication condition, leading to a 17.35% reduction in the filling ratio of the photonic crystal. A comparison of the stop gaps between radially polarized and linearly polarized beam illumination shows a higher suppression ratio in transmission and a wider wavelength range in the former case owing to the favorable tuning of the filling ratio of the three-dimensional photonic crystals. (C) 2009 Optical Society of America