  Hitchin's generalized complex geometry has been shown to be relevant in
compactifications of superstring theory with fluxes and is expected to lead to
a deeper understanding of mirror symmetry. Gualtieri's notion of generalized
complex submanifold seems to be a natural candidate for the description of
branes in this context. Recently, we introduced a field theoretic realization
of generalized complex geometry, the Hitchin sigma model, extending the well
known Poisson sigma model. In this paper, exploiting Gualtieri's formalism, we
incorporate branes into the model. A detailed study of the boundary conditions
obeyed by the world sheet fields is provided. Finally, it is found that, when
branes are present, the classical Batalin--Vilkovisky cohomology contains an
extra sector that is related non trivially to a novel cohomology associated
with the branes as generalized complex submanifolds.
