The astrophysical uncertainties in the distribution of dark matter in the halo of the Milky Way complicate the interpretation of dark matter direct and indirect detection data, and prevent a precise determination of the properties of the dark matter particle. Realistic cosmological simulations of galaxy formation including baryons have recently become possible, and provide important information on the properties of the dark matter halo. I will discuss the dark matter density and velocity distribution of Milky Way-like galaxies extracted from high resolution hydrodynamic simulations. To make reliable predictions for direct and indirect detection searches, we identify simulated galaxies which satisfy the Milky Way observational constraints. Using the dark matter distribution obtained from the selected Milky Way-like galaxies, I will present an analysis of direct detection data, discuss the possibility of dark disks, and the implications for the dark matter interpretation of the Fermi GeV excess.