Encapsidation of cellular- or plasmid-derived DNA sequences during recombinant adeno-associated virus (rAAV) production has been well documented. However, most of the published data were generated from rAAV vectors manufactured by the plasmid transient transfection method. We previously reported a novel, scalable method for rAAV manufacturing based on a recombinant herpes simplex virus (rHSV) complementation system. In this report, we evaluated clearance of DNA impurities during rAAV purification, by determining the quantity of residual herpes simplex virus and cellular DNA at each process step. A single Benzonase treatment during the upstream process effectively reduced unprotected HSV and cellular DNA to <300 bp fragments, and subsequent chromatography steps completely removed these small DNA fragments. Further analysis showed that trace amounts of residual, DNase-resistant HSV and cellular DNA were present at static concentrations during subsequent purification steps, and the residual HSV DNA sequences were single stranded, ranging from 0.8 to 4.2 kb. After transduction of human embryonic kidney 293 cells with purified rAAV, the residual HSV DNA fragments were neither transcribed nor translated into HSV proteins. In summary, this manufacturing process for rAAV production was effective in removing DNA and protein contaminants and achieving a highly purified product, suitable for human clinical application.