Secondary phase precipitates of a Zircaloy sample have been characterised by X-ray microspectroscopy. In Zircaloy-2 X-ray microscopy reveals pictures with a 40 nm resolution identifying Fe, Cr and to a lower occurrence Ni phases up to size of the micrometer. Analysis by X-ray spectroscopy defines the structure of specific secondary phase precipitates. The feasibility tests demonstrate that the characterisation of Fe and Cr can be performed on 100 nm size phases allowing the analysis of the Fe or Cr atoms environment in these secondary phase precipitates.