We report a novel transient instability upon temperature quench in weakly ordered block copolymer microphases possessing a soft direction or directions, such as the lamellar and hexagonal cylinder (HEX) phases. We show that reequilibration of the order parameter is accompanied by transient long wavelength undulation of the layers or cylinders-with an initial wavelength that depends on the depth of the temperature quench-that eventually disappears as the structure reaches its equilibrium at the new temperature. Such undulation leads to a transient transverse broadening of the scattering peaks near the Bragg positions. We argue that this instability might be responsible for the experimentally observed unusual ordering dynamics of the HEX phase of a diblock copolymer after quenching from the disordered state.