Circular dichroism (CD) spectra of small molecular aggregates, taking monomer vibrational motion into account, are calculated by employing wave packet propagation techniques. The spectra are related to the population and exciton transfer in the aggregates. It is investigated as to how far this dynamics can be directly extracted from the CD spectra. The method is applied to aggregates of perylene bisimides where temperature dependent spectra have recently been recorded in our laboratory [V. Dehm et al., Org. Lett. 9, 1085 (2007)].