The gene therapy landscape has exploded in the last few years, bringing a multitude of viral vectors to the clinic. At the forefront of this evolution is the application of lentivirus, adeno and adeno-associated virus (AAV), and plasmid-based therapies to genetic diseases of all types. With each program that progresses through the clinic, the body of manufacturing and clinical knowledge grows – and so does the availability of regulatory guidance. Adeno-associated virus (AAV) is increasingly popular, and the baculovirus-Sf9 platform has been established as a promising alternative to mammalian cell-based methods. However, the Sf9 baculovirus production system poses some unique analytical challenges. Here, we will discuss two of these issues – quantifying residual DNA and detecting the adventitious agent Sf-rhabdovirus – and solutions developed by Thermo Fisher Scientific designed to meet regulatory guidelines and ensure product quality and safety when utilizing the baculovirus-Sf9 platform for AAV production.