For drug substances manufactured in cell lines, host cell DNA is a common contaminant and its level must be carefully monitored. While residual DNA assays have been developed for many production cell lines, a robust assay is unavailable for baby hamster kidney (BHK) cells. The lack of genomics data of Syrian hamster, the origin of BHK cells, makes it challenging to design primers and probes for PCR-based methods. In this paper, we identified intracisternal A-particle (IAP) as an efficient PCR target for BHK DNA. PCR against IAP has been tested with conventional qPCR as well as with the recently developed ddPCR method, both of which demonstrated good efficiency with purified BHK DNA. However, the ddPCR-based method is less prone to matrix interference and is significantly more accurate than qPCR when testing complex samples, including multiple process intermediates. This study not only established a robust assay for the detection of residual BHK DNA, but also evaluated the capability of ddPCR technology for a new application.