Recent developments in nanoscience and nanotechnology significantly help improve the properties of traditional materials. A striking example of this is the formation of hybrid nanostructures based on nanoparticles and photosensitizer molecules, the potential range of applications of which extends from photovoltaics to biomedicine. However, the creation of new and effective hybrid nanomaterials of this form inevitably entails new challenges, one of which is a common and critical problem of aggregation of both nanoparticles and photosensitizer molecules. Therefore, a fundamental challenge is to determine the presence of these aggregates, which will produce a significant step toward creating a new generation of materials and devices of broad-spectrum applicability. Here we report on the key role of circular dichroism spectroscopy as a tool to detect the formation of nonluminescent aggregates of chlorin e6, a second-generation photosensitizer, in a hybrid nanostructure with ZnS:Mn quantum dots. These aggregates are active acceptors of photoexcitation energy from quantum dots and limit the photophysical properties of the whole nanostructure. It has been established that circular dichroism spectroscopy reveals the presence of nonluminescent molecule aggregates at chlorin e6 concentrations of ∼10-6 mol/L, which compares very favorably to absorption spectroscopy which does not show any direct indications of aggregation up to ∼10-5 mol/L. This result demonstrates the promise and importance of using circular dichroism spectroscopy in the study of organic/inorganic hybrid nanostructures.