We propose a way of relating CP violation in the quark and in the lepton sectors, that as usual we parametrize by the CKM and PMNS phases. If the origin of the CP breaking is in the complex Yukawa couplings, both in the quark and lepton sectors, the previous relation will not be possible in general, since Yukawa couplings in the two sectors have independent flavour structures. We will show that both the δ_CKM and δ_PMNS phases can instead be generated by a vacuum phase in a class of two Higgs doublet models, and in this case a connection may be established. This scenario requires, both in the quark and lepton sectors, the presence of scalar FCNC at tree level. The appearance of these FCNC is an obstacle since one has to analyse which models are able to conform to the strict experimental limits on FCNC, both in the quark and lepton sectors. On the contrary, this class of models is falsifiable since FCNC arise at a level which can be probed experimentally in the very near future, especially in processes like h→e^± τ^∓ and t→hc. The connection between CP violations in δ_CKM and δ_PMNS is explicitly illustrated in models with Minimal Flavour Violation with very interesting predictions.