In this review article we will present the application of Circular Intensity Differential Scattering (CIDS) and Differential Polarization Imaging (DPI), to the study of the ultrastructure of thylakoid membranes in chloroplasts. The results obtained provide new insight into the interpretation of the circular dichroism (CD) signals of chloroplasts, the macro-organization of thylakoid membranes, and into the possible mechanisms to regulate photosynthetic efficiency.