Since Faraday's founding work in 1831, it is known that the surface of a vertically vibrated fluid layers undergoes the Faraday instability when the forcing acceleration is greater than some critical value. Surface waves appear at the surface and form geometrical patterns characterised by a critical wavelength. We focus on the behaviour in complex fluids to such a hydrodynamic instability. Whe show that a strong coupling between the instability and the fluid microstructure may occur depending on the complex fluid. In semi-dilute wormlike micelles solutions, this coupling gives rise to standing elastic waves. In dilute wormlike micelles solutions, a shear-thickening phenomenom may be induced by the surfaces waves. And in suspensions of rod-like colloids localised alignment takes place.