A procedure was developed for the determination of low levels of the anthraquinones aloe-emodin and aloin A (barbalin) in aloe products based on gas chromatography/mass spectrometry (GC/MS) of the trimethyl silyl (TMS) derivatives of these analytes in the presence of Chrysophanol used as internal standard. The method was used to analyze several aloe based commercial products (liquids, gels and solids). Wide variation in the level of these anthraquinones was observed among the different products. The method had a sensitivity of 0.005 ppm of aloe-emodin and 0.05 ppm of aloin.