  In this paper we prove a special case of the Andr\'e-Oort conjecture for Kuga
varieties. If $M$ is a Kuga variety fibred over a pure Shimura variety $S$ as
an abelian scheme, and $(M_n)$ is a sequence of special subvarieties in $M$
which are faithfully flat over $S$, then the Zariski closure of the union of
the $M_n$'s is a finite union of special subvarieties faithfully flat over $S$.
The proof is reduced to a variant of the Manin-Mumford conjecture for abelian
schemes.
