  Using 3D radiative MHD simulations and Lyman-$\alpha$ transit calculations,
we investigate the effect of magnetic fields on the observational signatures of
atmospheric escape in exoplanets. Using the same stellar wind, we vary the
planet's dipole field strength ($B_p$) from 0 to 10G. For $B_p<3$G, the
structure of the escaping atmosphere begins to break away from a comet-like
tail following the planet ($B_p=0$), as we see more absorbing material above
and below the orbital plane. For $B_p\geq3$G, we find a ``dead-zone'' around
the equator, where low velocity material is trapped in the closed magnetic
field lines. The dead-zone separates two polar outflows where absorbing
material escapes along open field lines, leading to a double tail structure,
above and below the orbital plane. We demonstrate that atmospheric escape in
magnetised planets occurs through polar outflows, as opposed to the
predominantly night-side escape in non-magnetised models. We find a small
increase in escape rate with $B_p$, though this should not affect the timescale
of atmospheric loss. As the size of the dead-zone increases with $B_p$, so does
the line centre absorption in Lyman-$\alpha$, as more low-velocity neutral
hydrogen covers the stellar disc during transit. For $B_p<3$G the absorption in
the blue wing decreases, as the escaping atmosphere is less funnelled along the
line of sight by the stellar wind. In the red wing (and for $B_p>3$G in the
blue wing) the absorption increases caused by the growing volume of the
magnetosphere. Finally we show that transits below and above the mid-disc
differ caused by the asymmetry of the double tail structure.
