The stability of a rotor system presenting a transverse breathing crack is studied by considering the effects of crack depth, crack location and the shaft's rotational speed. The harmonic balance method, in combination with a path-following continuation procedure, is used to calculate the periodic response of a non-linear model of a cracked rotor system. The stability of the rotor's periodic movements is studied in the frequency domain by introducing the effects of a perturbation on the periodic solution for the cracked rotor system. It is shown that the areas of instability increase considerably when the crack deepens, and that the crack's position and depth are the main factors affecting not only the non-linear behaviour of the rotor system but also the different zones of dynamic instability in the periodic solution for the cracked rotor. The effects of some other system parameters (including the disk position and the stiffness of the supports) on the dynamic stability of the non-linear periodic response of the cracked rotor system are also investigated.