We report the alignment and shape of dark matter, stellar, and hot gas distributions in the EAGLE and cosmo-OWLS simulations. The combination of these state-of-the-art hydro-cosmological simulations enables us to span four orders of magnitude in halo mass ($11 < log_{10}(M_{200}/ [h^{-1}M_odot]) < 15$), a wide radial range ($-2.3 < log_{10}(r/[h^{-1}Mpc ]) < 1.3$) and redshifts $0 < z < 1$. The shape parameters of the dark matter, stellar and hot gas distributions follow qualitatively similar trends: they become more aspherical (and triaxial) with increasing halo mass, radius and redshift. We measure the misalignment of the baryonic components (hot gas and stars) of galaxies with their host halo as a function of halo mass, radius, redshift, and galaxy type (centrals vs satellites and early- vs late-type). Overall, galaxies align well with the local distribution of the total (mostly dark) matter. However, the stellar distributions on galactic scales exhibit a median misalignment of about 45-50 degrees with respect to their host haloes. This misalignment is reduced to 25-30 degrees in the most massive haloes ($13 < log_{10}(M_{200}/ [h^{-1}M_odot ]) < 15$). Half of the disc galaxies in the EAGLE simulations have a misalignment angle with respect to their host haloes larger than 40 degrees. We present fitting functions and tabulated values for the probability distribution of galaxy-halo misalignment to enable a straightforward inclusion of our results into models of galaxy formations based on purely collisionless N-body simulations.