The new automated differential extraction method resembles the standard organic extraction method, in that it begins with differential proteinase K lysis and centrifugation to pellet undigested sperm. Following removal of a nonsperm fraction from the digest supernatant, the automated method diverges from the standard method. Paramagnetic resin is used to cap and immobilize the sperm pellet at the bottom of the plate-well, using a strong magnet. The nonsperm DNA in the supernatant is washed away by the liquid-handling platform without disturbing the sperm pellet. The resin will not bind DNA until the subsequent addition of lysis buffer. After pellet washing, a layer of a nonaqueous Separation Solution is added to the remaining wash volume, separating it and any trapped nonsperm DNA by phase from the sperm pellet below. Pellet capping coupled with distinct phase separation reduces guesswork and technique-dependent variability for analysts, while preserving sperm-fraction DNA yield. This process deviates from the original protocol described for manual Differex processing, in which the sperm pellet was centrifuged directly through the Separation Solution; and it significantly improves DNA yield from the sperm pellet. This method offers several advantages over traditional phenol: chloroform extraction. The chemistry is nontoxic and biodegradable, so it can be used in an open environment and disposed of easily. In contrast to other methods, minimal washing and centrifugation steps are required, leading to reduced time and labor costs. The speed of processing and consistency are improved. 2 figures