We discuss systematically the fermion mass and mixing matrices in a generic field-theoretical flipped SU(5) model, with particular applications to neutrino and baryon number-changing physics. We demonstrate that the different quark flavour branching ratios in proton decay are related to the Cabibbo-Kobayashi-Maskawa angles, whereas the lepton flavour branching ratios are undetermined. The light neutrino mixing angles observable via oscillation effects are related to the heavy conjugate (right-handed) neutrino mass matrix, which also play a key role in cosmological baryogenesis. The ratios of neutrino and charged lepton decay modes in baryon decay may also be related to neutrino oscillation parameters. Plausible Ansätze for the generation structure of coupling matrices motivate additional relations between physical observables, and yield a satisfactory baryon asymmetry.