Abstract: Disclosed is a rapid, dual purpose, PCR-based method for identifying two or more pathogens, including Giardia and/or Cryptosporidium, in an extracted sample, such as stool or environmental (soil, water) isolates, in individual real-time PCR reactions. This method is of particular utility for clinical, veterinary, and environmental testing applications. The present methods are more sensitive than conventional ELISA or IFA-based methods of detection. An internal control (IC) for use in the PCR based nucleic acid detection method is also disclosed.