  We discuss the structure of Yukawa couplings in D-brane models in which the
SM fermion spectrum appears at the intersections of D-branes wrapping a compact
space. In simple toroidal realistic examples one can explicitly compute the
Yukawa couplings as a function of the geometrical data summing over world-sheet
instanton contributions. A particular simple model with a N = 1 SUSY spectrum
and three quark-lepton generations is studied in some detail. Remarkably, one
can reproduce the observed spectrum of quark masses and mixings for particular
choices of the compact radii and brane locations. In order to reproduce the
smallness of up- and down-quark masses branes should be located in simple
geometric configurations leading to some accidental global symmetries. We also
find that the brane configurations able to reproduce the observed data may be
considered as a deformation (by brane translation) of a configuration with
Pati-Salam gauge symmetry. The origin of CP-violation in this formalism is
quite elegant. It appears as a consequence of the generic presence of U(1)
Wilson line backgrounds in the compact dimensions. One can reproduce the
observed results for the CP-violation Jarlskog invariant J as long as the
compact radii are of order of the string scale.
  DISCLAIMER: This paper is going to be substantially revised. Althought the
physics and general concepts are still valid, the Yukawa couplings of the
particular model presented in this paper have a simpler form than discussed
here, as we recently pointed out in hep-th/0302105. A properly revised version
will be eventually sent as the paper is appropriately corrected.
