Recombinant Adeno-associated Virus is one of the leading platforms for monogenic disease therapy. One of the attractive features of rAAV is its wide tropism, owing in part to its surface property where charged amino acids are not conserved. In addition, charged regions are also involved during its transduction of host cells. As a result, the characterization of its charged surface is necessary for understanding of rAAV function. Here we present the exploration of the charge profile of rAAV and give a fingerprint of the charge profile, and demonstrate the potential application of charge fingerprinting for formulation development under elevated temperature and pH stress.