Silicon nanotubes (SiNTs) are compatible with Si-based semiconductor technology. In particular, the small diameters and controllable structure of such nanotubes are remaining challenges. Here we describe a method to fabricate SiNTs intrinsically connected with cobalt silicide ends based on highly ordered anodic aluminum oxide (AAO) templates. Size and growth direction of the SiNTs can be well controlled via the templates. The growth of SiNTs is catalyzed by the Co nanoparticles reduced on the pore walls of the AAO after annealing, with a controllable thickness at a given growth temperature and time. Simultaneously, cobalt silicide forms on the bottom side of the SiNTs.