We consider a class of N=1 supersymmetric extensions of the Standard Model in which the soft breaking sector is CP conserving at the GUT scale. We study the question of whether the presence of explicit CP violation in the Yukawa sector of the theory induces through renormalization effects CP violating phases in the soft terms, which could lead to observable effects. A clear pattern appears in the structure of phases in the soft sector. In particular, the inclusion of intergenerational mixing

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... uces large phases in the flavour mixing entries of the trilinear soft breaking terms, whereas the diagonal entries remain real. A mechanism is proposed for generating through chargino exchange a contribution to the neutron electric dipole moment which can be a few orders of magnitude larger that that of the Standard Model, although still out of reach of experimental tests. We comment on the possible relevance of these phases for baryogenesis at the weak scale in minimal supersymetric scenarios, recently considered in the literature.