  We study the problem of instanton generated superpotentials in Calabi-Yau
orientifold compactifications directly in type IIB string theory. To this end,
we derive the Dirac equation on a Euclidean D3 brane in the presence of
background fluxes. We propose an index which governs whether the generation of
a superpotential in the effective 4d theory by D3 brane instantons is possible.
Applying the formalism to various classes of examples, including the K3 x
T^2/Z_2 orientifold, in the absence and presence of fluxes, we show that our
results are consistent with conclusions attainable via duality from an M-theory
analysis.
