Carotenoids play an important role of light harvesting, photoprotection and structural stabilization in the photosynthetic organisms. Despite their functional importance, the molecular basis for binding of carotenoids in the photosynthetic pigment-protein complexes is poorly understood. On the basis of a recent discovery that carotenoids are surrounded either by aromatic residues or by chlorophylls in all known crystal structures of the photosynthetic pigment-protein complexes (J. Am. Chem. Soc. 2002, 124, 8445), it is hypothesized that pi-pi stacking interactions are the molecular forces that bind carotenoids in the photosynthetic pigment-protein complexes. In this article, the pi-pi stacking interactions between the carotenoid molecule peridinins and their surrounding aromatic groups (aromatic residues and chlorophyll-a) in the peridine-chlorophyll-protein complex of Amphidinium carterae are characterized by means of the supermolecular approach with the second-order Moller-Plesset perturbation method (MP2). The modified 6-31G*(0.25) basis set with diffuse d-polarization by Hobza et al. is adopted here. A representative peridinin chlorophyll pair (PID624...Chl602) is chosen to study the structural stabilization role of peridinin, and three unique peridinin and aromatic residue pairs (PID623...TYR270, PID624...PHE301, and PID624...PHE304) are chosen to study the configurational (orientation and distance) dependence of pi-pi stacking interactions between peridinins and their interacting partners. The MP2/6-31G*(0.25) calculations yielded a favorable pi-pi stacking interaction energy of -11.52 kcal/mol between the large conjugated tetrapyrrol pi-system of chlorophyll Chl602 and the long conjugated pi-electrons of peridinin PID624. For the parallelly oriented PID623...TYR270 pair, the MP2/6-31G*(0.25) calculations give rise to a stabilization energy of -7.25 kcal/mol. For the perpendicularly oriented pairs, the calculated MP2/6-31G*(0.25) pi-pi stacking energies are -3.77 and -1.71 kcal/mol for PID624...F301 and PID624...F304, respectively. It is thus concluded that pi-pi stacking interactions between peridinins and the nearby aromatic groups play a substantial role in binding peridinins in the peridine-chlorophyll-protein complex of A. carterae. Consequently, the molecular basis of the structural stabilization function of carotenoids in forming the pigment-protein complexes is unraveled.