  In Conformal Field Theories with a gravitational AdS dual it is possible to
calculate the entanglement entropy of a region $A$ holographically by using the
Ryu-Takayanagi formula. In this work we consider systems that are in a pure
state that is not the vacuum. We study in particular the 2D Conformal Field
Theory dual to type IIB string theory on AdS$_3 \times S^3 \times T^4$ and
focus on the $1/4$-BPS states described holographically by the 2-charge
microstate geometries. We discuss a general prescription for the calculation of
the entanglement entropy in these geometries that are asymptotically AdS$_3
\times S^3$. In particular we study analytically the perturbative expansion for
a single, short interval: we show that the first non-trivial terms in this
expansion are consistent with the expected CFT structure and with previous
results on the vevs of chiral primary operators for the $1/4$-BPS
configurations.
