GaN/AlN stacked quantum dots have been studied by means of Cathodoluminescence and Transmission Electron Microscopy. Assignment of the optical emissions was made on the basis of the structural parameters and power dependent cathodoluminescence studies. Quantum dot layer (depending on the nominal GaN coverage) and buffer layers emissions were distinguished. A quantum dot size dependent blue shift and a saturation trend was observed by increasing the power injection conditions. An important difference, both in structural and optical properties, among the isolated and the stacked quantum dots layers was also evidenced.