We investigate the spatial distribution and emission properties of self-assembled GaN/AlN quantum dots. High-resolution transmission electron microscopy reveals near vertical correlation among the GaN dots due to a sufficiently thin AlN spacer layer thickness, which allows strain induced stacking. Scanning electron and atomic force microscopy show lateral coupling due to a surface roughness of ∼ 50–60 nm. Near-field photoluminescence in the illumination mode (both spatially and spectrally resolved) at 10 K revealed emission from individual dots, which exhibits size distribution of GaN dots from localized sites in the stacked nanostructure. Strong spatial localization of the excitons is observed in GaN quantum dots formed at the tip of self-assembled hexagonal pyramid shapes with six [101 1] facets.