Ternary InGaN nanorods were prepared on dielectric-masked nano-holes with selective area metalorganic chemical vapor deposition. To overcome the tendency for random nucleation of GaN at low temperatures, a pulsed growth procedure was introduced to enhance the diffusion length of Ga adatoms on SiO2, resulting in good selectivity at typical temperature ranges for InGaN. Photoluminescence from the InGaN nanorods can be tuned from near ultraviolet (400 nm) to blue-green (~500 nm). Microstructural properties were characterized by transmission electron microscopy; threading dislocations from the underlying GaN template were terminated at the nanorod/template interface, resulting in dislocation-free nanorods. The height of dislocation-free InGaN nanorods is about 150 nm, which is much larger than the critical thickness for the onset of misfit dislocations in planar InGaN growth with typical thickness of less than 10 nm for an indium composition between 10 and 20%. The composition profile of In along the growth direction was examined by energy dispersive x-ray spectroscopic mapping and line scan. Oscillations of In composition along the growth direction were observed and are likely due to the kinetic competition between In and Ga adatoms. These InGaN nanorods are expected to be useful as templates for growing higher In composition nano-light-emitting diodes.