An overview of investigations on unusual atomic systems, such highly charged ions and pionic atoms, is presented. In highly charged ions, where the associated Coulomb field is several order of magnitude higher that of the most powerful available laser, Quantum Electrodynamics (QED) corrections, as the self-energy and the vacuum polarisation, have to be considered to all order of Zα. This is still a challenge for theoretical predictions, which can finely tested by spectroscopy of such systems. In pionic hydrogen and deuterium, high-accuracy X-ray spectroscopy provides important information on the strong interaction force between the pion (formed by an anti-quark and a quark) and the nucleons (proton and/or the neutron, each formed by three quarks). Experimental findings are compared to the more accurate available predictions based on effective field theories. In the case of atomic transitions where the influence of the strong force is negligible and QED predictions are well known, accurate X-ray spectroscopy is used to determine the mass of the negatively charged pion. The new measurement presented here yields an accuracy of 1.3 parts per million improving the accuracy of the value recommended by the Particle Data Group by a factor of about two.