We describe the use of electron channelling contrast imaging (ECCI) – in a field emission scanning electron microscope (SEM) – to reveal and identify defects in nitride semiconductor thin films. In ECCI changes in crystallographic orientation, or changes in lattice constant due to local strain, are revealed by changes in grey scale in an image constructed by monitoring the intensity of backscattered electrons (BSEs) as an electron beam is scanned over a suitably oriented sample. Extremely small orientation changes are detectable, enabling small angle tilt and rotation boundaries and dislocations to be imaged. Images with a resolution of tens of nanometres are obtainable with ECCI. In this paper, we describe the use of ECCI with TEM to determine threading dislocation densities and types in InAlN/GaN heterostructures grown on SiC and sapphire substrates.