The backlog of untested sexual assault kits (SAKs) has become a major crisis, resulting in hundreds of thousands of unresolved cases across the United States. The processing of SAKs relies on the genetic analysis of material extracted from gynecological swabs collected from the assault victim. A vital step in producing an identifiable DNA profile of the perpetrator, is the effective separation of perpetrator (male) and victim (female) DNA from the collected evidence. In this work, a capillary zone electrophoresis system was developed for the separation of intact sperm from whole and lysed epithelial cells in SAKs. The separated components were deposited into individual wells of a microtiter plate using a computer-controlled fraction collector, and quantitative PCR was used to verify the collection of sperm cells by targeted amplification of male DNA. The technology was verified with simulated sexual assault samples that were aged for up to 18 months, as well as vaginal swabs from authentic forensic kits, demonstrating a clean separation and collection of sperm cells for downstream analysis.