Electron microscopy methods have been used in recent collaborative studies to investigate the defect microstructure of III-nitride materials and devices. An approach based on convergent beam diffraction allowed the elemental composition of pseudomorphic InGaN/GaN quantum well structures to be determined on the nanometer scale. Indium compositional fluctuations in InGaN quantum wells caused local electric field inhomogeneities that seemed to be more pronounced near the onset of InGaN layer growth, suggesting strain relaxation as a strong contributing factor.. Relaxed InN quantum dots were invariably associated with threading dislocations in the underlying GaN buffer layer, and the interfacial misfit was accommodated by periodic dislocation arrays. Lateral phase separation in InAlN/GaN heterostructures possibly originating from misfit-strain relaxation at the heterointerface, resulted in the development of a vertical 'honeycomb' structure. The structural and electronic properties of AlGaN/GaN heterostructures grown by molecular beam epitaxy have been correlated with the Al/N flux ratio during nucleation layer growth. Electron microscopy played a central role in contributing to the development of ferromagnetic Cr-doped nitride semiconductors.