We investigate the relative photo-damage effects during one- and two-photon excitations and demonstrate that there exist fundamental differences in the damage induced by a high repetition rate laser as compared to that of a CW laser. This difference is evident from the degree of enhanced fluorescence intensity achieved by blanking the excitation with an optical chopper. Such an enhancement in fluorescence intensity provides better signal-to-noise ratio that could have immediate applications in multiphoton imaging of live specimens.