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This paper briefly discusses two current projects relevant to waterborne Cryptosporidium parvum detection and identification. The first project involves the development of polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) markers for fingerprinting C. parvum. The goals of this project are to identify the primary routes of transmission of C. parvum leading to human infections and to provide a means of identifying sources of oocyst contaminations. The second project is intended to improve PCR detection methods for waterborne oocysts and could provide the water industry with a method to determine whether oocysts found in surface water originate from human or animal sources.