  We explore contributions to the 4D effective superpotential which arise from
Euclidean D3 branes (``instantons'') that intersect space-filling D-branes.
These effects can perturb the effective field theory on the space-filling
branes by nontrivial operators composed of charged matter fields, changing the
vacuum structure in a qualitative way in some examples. Our considerations are
exemplified throughout by a careful study of a fractional brane configuration
on a del Pezzo surface.
