Transmission and scanning electron microscopy are used to examine the role of an intermediate nanorod layer in reducing threading defect densities in GaN/(0001)sapphire. Films grown by molecular beam epitaxy under N-rich conditions showed Ga-polar nanorods growing out of a more compact N-polar layer. The nanorods sometimes contained extended threading defects, which were faulted dipoles lying on {10-10} planes with a displacement vector of ±1/2[0001], which act as sources for spiral growth. By overgrowing the nanorods under Ga-rich conditions, continuous epilayers were formed with threading defect densities down to 108 cm−2. In a second approach, nanorods produced by etching through a self-organised layer of Ni islands were overgrown by metal-organic chemical vapour deposition, to produce overlayers with defect densities down to 5*107 cm−2. In both cases, the mechanisms by which the nanorod layer reduces the threading defect density are identified.