AbstractWe have studied the large scale distribution of matter in the Chandra Deep Field South on the basis of photometric redshifts and we have identified several over-densities between redshift 0.6 and 2.3. We analyse two of these structures using the deepest X-ray observations ever obtained: 4 Ms with the Chandra satellite and 2.5 Ms with XMM-Newton. We set a very faint upper limit on the X-ray luminosity of a structure at redshift 1.6, and we find an extended X-ray emission from a structure at redshift 0.96 of which we can estimate the gas temperature and make a comparison with the scaling relations between the X-ray luminosity and mass or temperature of high redshift galaxy clusters.