The interplay between magnetism and electron transport in atomic-scale nanosystems is presently of considerable interest being at the origin of many intriguing phenomena such as giant magnetoresistance, anisotropic magnetoresistance, spin filtering, Kondo physics at low temperatures, etc. To tackle this kind of problems we have developed the DFT (Density functional theory) approach for calculating the ballistic conductance in nanosystems implemented within the plane wave package Quantum-ESPRESSO [1]. The method was recently applied to multiferroic tunnel junctions [2], predicting four distinct resistance states, and to Pt monatomic nanocontacts [3], which were shown to develop magnetic ordering with a large anisotropy energy. More recently, we have started looking at the transport properties of locally magnetic nanosystems consisting of two nonmagnetic bulk conductors bridged by some magnetic structure. To get insight into low temperature Kondo physics we combine [4] our DFT approach with Numerical renormalization group calculations. We exemplify our method on a case of a single magnetic atom (Ni, Co) adsorbed on a Au nanowire [4], a Cu surface, or a carbon nanotube. [1] P. Giannozzi et al., http://www.quantum-espresso.org. [2] J. Velev et al., Nano Letters 9, 427 (2009). [3] A. Smogunov et al., Nature Nanotechnology 3, 22-25 (2008); A. Smogunov et al., Phys. Rev. B 78, 014423 (2008). [4] P. Lucignano et al., to appear in Nature Materials.