A new method for sensitive determination of protein secondary structure via multi-photon absorption is considered theoretically. Perturbation theory is developed to describe the polarization-dependent two-photon absorption (TPA) of alpha-helix and beta-sheet protein secondary structures. The exciton coupling interactions responsible for relatively weak electronic circular dichroism in one-photon absorption are predicted to give rise to large changes in the TPA cross-section (>200%) for circular versus linear incident polarizations, defined as CLD. The CLD effect in TPA is electric dipole-allowed, which explains the much greater sensitivity. These predictions suggest TPA should be a viable means of sensitively probing protein secondary structure. (C) 2008 Elsevier B.V. All rights reserved.