We demonstrate alignment and positional control of gold nanorods grown in situ on substrates using a seed-mediated synthetic approach. Alignment control is obtained by directing the growth of spherical nanoparticle seeds into nanorods in well-defined poly(methyl methacrylate) nanochannels. Substrates with prepatterned metallic electrodes provide an additional handle for the position of the gold nanorods and yield nanometer-sized gaps between the electrode and nanorod. The presented approach is a novel demonstration of bottom-up device fabrication of multiple nanogap junctions on a single chip mediated viain situ growth of gold nanorods acting as nanoelectrodes.