Increased health concerns about perchlorate (ClO4-) during the past decade and subsequent regulatory considerations have generated appreciable interest in source identification. The key objective of the isotopic techniques described in this guidance manual is to provide evidence concerning the origin of ClO4- in soils and groundwater and, more specifically, whether that ClO4- is synthetic or natural. Chlorine and oxygen isotopic analyses of ClO4- provide the primary direct approach whereby different sources of ClO4- can be distinguished from each other. These techniques measure the relative abundances of the stable isotopes of chlorine (37Cl and 35Cl) and oxygen (18O, 17O, and 16O) in ClO4- using isotope-ratio mass spectrometry (IRMS). In addition, the relative abundance of the radioactive chlorine isotope 36Cl is measured using accelerator mass spectrometry (AMS). Taken together, these measurements provide four independent quantities that can be used to distinguish natural and synthetic ClO4- sources, to discriminate different types of natural ClO4-, and to detect ClO4- biodegradation in the environment. Other isotopic, chemical, and geochemical techniques that can be applied in conjunction with isotopic analyses of ClO4- to provide supporting data in forensic studies are also described.