Compton scattering within the accretion column of magnetic cataclysmic variables (mCVs) can induce a net polarization in the X-ray emission. We investigate this process using Monte Carlo simulations and find that significant polarization can arise as a result of the stratified flow structure in the shock-ionized column. We find that the degree of linear polarization can reach levels up to ~8% for systems with high accretion rates and low white-dwarf masses, when viewed at large inclination angles with respect to the accretion column axis. These levels are substantially higher than previously predicted estimates using an accretion column model with uniform density and temperature. We also find that for systems with a relatively low-mass white dwarf accreting at a high accretion rate, the polarization properties may be insensitive to the magnetic field, since most of the scattering occurs at the base of the accretion column where the density structure is determined mainly by bremsstrahlung cooling instead of cyclotron cooling. ; Comment: 7 pages, 8 figures, accepted by MNRAS