While high harmonic generation from atoms is relatively well understood, the ability to align gas-phase molecules opens an opportunity to more deeply understand the underlying physics. Many assumptions, such as the single active electron approximation, neglect of the Coulomb potential, the strong field approximation, and the assumption of plane waves, are being challenged by new experimental observations. We study high harmonic emission from aligned molecules such as N₂, O₂ and CO₂. We present experimental measurements of the amplitude of the emission as a function of molecular angle, as well as the polarization state.