  Quantum entanglement in 3 spatial dimensions is studied in systems with
physical boundaries when an entangling surface intersects the boundary. We show
that there are universal logarithmic boundary terms in the entanglement
R\'{e}nyi entropy and derive them for different conformal field theories and
geometrical configurations. The paper covers such topics as spectral geometry
on manifolds with conical singularities crossing the boundaries, the dependence
of the entanglement entropy on mutual position of the boundary and the
entangling surface, effects of acceleration and rotation of the boundary,
relations of coefficients in the trace anomaly to coefficients in the boundary
logarithmic terms in the entropy. The computations are done for scalar, spinor
and gauge fields.
