X-ray Emission Techniques (EDXRF) and External Proton Induced X-ray Emission Technique (PIXE) have been used to characterize 13 gem stones obtained from Gem Testing Laboratory, Jaipur, India. Radioisotope sources 109Cd and 241Am were used to excite the gem stones to generate K and L X-rays in the low and high Z region of the periodic table to investigate trace element inclusions besides the main matrix. A proton beam of 4 MeV energy and current of 8 nA intensity were extracted from the FOTIA (Folded Tandem Ion Accelerator) at VandeGaaff Accelerator, Trombay, Mumbai in air through a Kapton foil of 8 micrometer thick mounted on a Teflon cone. Gem stones such as Labradorite Feldspar, Moonstone Feldspar, Almandine Garnet, Tsavorite Garnet, Apatite, Natural Spinel, Natural Zircon, Spessartine Garnet, Natural Ruby (Lead filled), Natural Ruby were characterized for their elemental profile to see the differences in composition besides the main matrix differences. Elements such as Ca, Ti, V, Cr, Mn, Fe, Cu, Zn, Sr, Y and Zr were detected.