Atomic Force Microscopy and Grazing incidence X-ray diffraction measurements have revealed the presence of ripples aligned along the $[1bar{1}0]$ direction on the surface of (Ga,Mn)As layers grown on GaAs(001) substrates and buffer layers, with periodicity of about 50 nm in all samples that have been studied. These samples show the strong symmetry breaking uniaxial magnetic anisotropy normally observed in such materials. We observe a clear correlation between the amplitude of the surface ripples and the strength of the uniaxial magnetic anisotropy component suggesting that these ripples might be the source of such anisotropy.