In this study we investigate the appearance of etch pits and their effect on the ECV doping profiles of PM-HEMT structures grown by MOCVD and MBE. In some samples, etch-pits were observed after the etching of only 20 nm of the top layer. The observed pits had a circular pattern with diameter ranging from 2 to 25 μm. Study of these patterns by atomic force microscopy (AFM) showed that they are holes with a depth varying from 0.3 to 2 μm. The contribution of this hole area in the capacitance measurement during the ECV process results in the reduction and broadening of the observed peaks and in non reproducible profiling across the wafer. The dependence of the density and dimensions of the etch-pits on the etching depth are also presented.