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In the present study we report synthesis and investigation of the magnetic iron nanowire arrays in the mesoporous silica thin films. The films were deposited on SiC/Si(100) substrate by spin-coating technique, enabling one to obtain all mesopores parallel to the substrate surface and aligned radially by centrifugal force. Very high level of local alignment (90% on 2 cm2) of the pores was proved by small angle X-ray scattering and neutron reflectivity. Magnetic iron nanowires were synthesized in the mesoporous silica channels by intercalation of a hydrophobic iron compound into a hydrophobic part of the silica–surfactant composite followed by decomposition of the complex and additional crystallization of iron in hydrogen flow. Nanocomposites were studied by TEM, ED, SAXS, BET, BJH and neutron reflectometry. It was found that an ordered structure preserves after the chemical modification, while iron nanowires uniformly fill porous structure, making this system highly promising for high-density data recording media.