  Recent work on F-theory GUTs has shown that the predicted masses, and
magnitudes of the mixing matrix elements in the quark and lepton sectors are in
close accord with experiment. In this note we estimate the CP violating phase
of the mixing matrices by considering the Jarlskog invariant. We find by
carefully treating certain cancellations in the computation of the Jarlskog
invariant that |J_quark| ~ alpha_GUT^(3) ~ 6*10^(-5), and that the CP violating
phase of the quark sector is large, in accord with experiment. Moreover, we
predict (up to order one factors) that |J_lepton| ~ alpha_GUT ~ 4*10^(-2) and
that the CP violating phase of the lepton sector is also large.
