Localized brain proton magnetic resonance spectroscopy (MRS) has been performed using a STEAM (stimulated echo-acquisition mode) method with a short-echo time (20 ms) in 10 children suffering from different lysosomal diseases, 6 boys with X-linked adrenoleukodystrophy (X-ALD) and 5 healthy children. Metabolic data from localized spectra were processed by principal component analysis (PCA) of 7 metabolic variables recorded on the MR spectra. PCA allows to delineate different clusters corresponding to the 2 pathological groups which are separated from each other and from the control group. The position of each spectrum on the patient map correlates with the clinical data and to the evolution of the patients subjected to a follow-up. These results also confirm the metabolic features characterizing the pathologies of the lysosome (increase in inositol) and the peroxisome (increase in choline and free lipids). PCA constitutes an alternative to the classical statistical methods to analyze and compare metabolic modifications in small populations of patients and allows to identify the most critical parameters defining the organization of the pathological populations. This analysis clearly increases the discrimination among pathologies based on the metabolic profiles obtained by MRS.