The standard method for purifying sperm from swabs taken from rape victims is to resuspend first all cells and to digest selectively the excess of the victim's epithelial cells. The intact sperm are then separated from the contaminating solubilized DNA by centrifugation, careful removal of supernatant, and extensive washing of the sperm pellet; all of these steps are difficult to automate. The backlog of sexual assault cases in police departments is due in part to the labor intensive process used to isolate sperm DNA from casework samples. In the alternative procedure described in this paper, the initial steps required to elute cells from the swab cutting and to digest the epithelial cells involve only pipetting, shaking, and temperature controlled incubation, all of which can be done in a 96 deep well microtiter plate by a robotic workstation. The steps downstream of sperm purification of sexual assault cases have already been automated in a multi-array format, and the final steps of PCR amplification and fragment analysis by capillary electrophoresis are currently processed in high throughput formats for a variety of industrial genomic applications. Vacuum-driven filtration thus allows fully automated processing of the sexual assault case backlog. Plans are underway to compare this vacuum-based method directly with the standard protocol on nonprobative casework samples. 3 figures and 12 references