We show that electronic inhomogeneities in graphene lead to shifts in the phonon spectrum via the electron-phonon coupling. The frequency shifts in single layer samples are proportional to the square root of the local electronic density and can be measured directly in Raman spectroscopy. In samples with many layers, we find a shift proportional to the carrier concentration, and a splitting of the phonon frequencies if the charge is not homogeneously distributed. Our results may help to elucidate the nature of the disorder in graphene samples and its effect on electronic transport.