Red layered medieval stained glass windows on a transparent greenish substrate are characteristic of European medieval cathedrals, but few compositional analyses have been performed on the coloured layers. The PIXE technique has been performed on a red layered stained glass window obtained during the restoration works carried out in Las Huelgas Monastery in Burgos (Spain). Protons of 3MeV with a beam of 4×5μm 2 were used to acquire elemental maps of a cross section of the sample, in order to observe the homogeneity of the layered structure and its substrate.In our work, copper was detected as in other layered glasses but a correspondence with lower amounts of zinc has also been determined. Both elements appear enriched in the red coloured layers, while the other quantified elements have the same relative composition along the sample. Corrosion layers, due to the lead supporting structure of the window, were also found.