  We systematically investigate instanton corrections from wrapped Euclidean
D-branes to the matter field superpotential of various classes of N=1
supersymmetric D-brane models in four dimensions. Both gauge invariance and the
counting of fermionic zero modes provide strong constraints on the allowed
non-perturbative superpotential couplings. We outline how the complete
instanton computation boils down to the computation of open string disc
diagrams for boundary changing operators multiplied by a one-loop vacuum
diagram. For concreteness we focus on E2-instanton effects in Type IIA vacua
with intersecting D6-branes, however the same structure emerges for Type IIB
and heterotic vacua. The instantons wrapping rigid cycles can potentially
destabilise the vacuum or generate perturbatively absent matter couplings such
as proton decay operators, mu-parameter or right-handed neutrino Majorana mass
terms. The latter allow the realization of the seesaw mechanism for MSSM-like
intersecting D-brane models.
