We demonstrate that the MSSM flat directions can naturally account for the seed magnetic fields in the early Universe. The non-zero vacuum expectation value of an MSSM flat direction condensate provides masses to the gauge fields and thereby breaks conformal invariance. During inflation the condensate receives spatial perturbations and $SU(2) x U(1)_Y$ gauge currents are generated together with (hyper)magnetic fields. When these long wavelength vector perturbations reenter our horizon they give rise to $U(1)_{em}$ magnetic fields with an amplitude of $10^{-30}$ Gauss, as required by the dynamo mechanism.