Endotoxin is the most common contaminant found in protein samples. Even small amount of endotoxin can induce strong allergic reaction and death of a host organism. Endotoxin is also often detected in recombinant Adeno-associated virus (rAAV) stocks prepared in research laboratories using off-the-shelf reagents; purifying rAAV stocks from endotoxin using commercial reagents sometimes results in significant titer loss. The problem is exacerbated due to recently expanded diversity of rAAV serotypes and capsid variants which, due to their variable capsid surface charge, display differential affinity towards endotoxin. In this paper, we describe a simple universal protocol of purifying vector stocks irrespective of AAV serotype. The protocol is based on subjecting endotoxin-contaminated rAAV to mild detergent treatment followed by repeated buffer-exchange washing and concentrating viral stock by low speed centrifugation. Multiple assays were employed to test the physical and biological equivalency of the viral stocks before and after purification. The described protocol has been routinely utilized to purify vector stocks contaminated at the levels as high as >1,000 endotoxin units per mL (EU/mL) to produce viral vectors with practically undetectable levels of endotoxin (< 2.5 EU/mL) with the titer’s recovery in the range of 50-100%.