Abstract:  While molecular clouds are among the coldest objects in the Milky Way, an illumination by flares from Sgr A* turns them into powerful X-ray sources. By studying X-ray emission from molecular clouds we learn about the past activity of our Galactic Center over the last few hundred years. The same data provide unique probes of the inner structure of molecular clouds, such as, the density probability distribution function or line of sight positions, among others. We discuss constraints on clouds properties that are possible to place today as well as prospects of doing advanced diagnostics with future missions.