The aim of this work is to describe the structure and the composition of light emitting diode (LED) chips from Rutherford Backscattering Spectroscopy and Particle Induced X-ray Emission measurements performed with a 2 MeV He-4(+) micro-beam focused down to a 1 mum(2) spot size, We also investigated charge transport properties of GaN based LEDs by means of Ion Beam Induced Charge Collection. The spatial distribution of the charge collection in the chip is determined using a micro-beam with a low flux of less than 400 ions per second. The interaction of the incident ions induces the creation of electron-hole (e-h) pairs within the structure of the LED. The created charges are collected by the application of a reverse bias voltage. Since the technique allows an accurate localization of e-h pair creation sites, with a spatial resolution better than 1 mum(2), the obtained maps provide details on the structural heterogeneity of the p-n junction and on the structural quality of the LEDs.