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. This guidance manual is intended to provide details of the methodology used to (1) collect ClO4- samples from the environment, particularly from groundwater, which is the main medium of interest for ClO4- source identification; (2) purify the collected ClO4- samples; (3) conduct oxygen (O) and chlorine (Cl) isotopic analyses on the purified samples; and (4) determine probable sources using the resulting isotope data. Current practices for groundwater sampling and quality assurance for sample collection, purification, and measurement of Cl and O isotopes in ClO4- are provided. A detailed case study of source evaluation in groundwater on Long Island is given along with the current literature on the subject of ClO4- source discrimination. ClO4- in the environment is derived from both synthetic and natural sources. Synthetic ClO4- salts, including ammonium perchlorate (NH4ClO4) and potassium perchlorate (KClO4), have been widely used as oxidants by the military and aerospace industry. A variety of commercial products also contain synthetic ClO4-,including fireworks, matches, air bags, chlorine bleach, safety flares, perchloric acid, and chlorate herbicides. Historical disposal practices by the military, aerospace industry, and chemical manufacturers have resulted in groundwater and drinking water contamination with ClO4- in the United States. Isolated contamination from fireworks, road flares, explosives, and perchloric acid has also been reported. However, ClO4- is also a naturally occurring anion. It is present with sodium nitrate (NaNO3) in surficial deposits in the Atacama Desert of Chile at an average concentration of around 0.1% (by mass) of the total soluble salt, and these deposits (sometimes referred to as “Chilean caliche”) were widely used in the United States during the first half of the 20th century as a source of inorganic nitrogen fertilizer. Natural ClO4- that is not associated with Chilean fertilizers has also recently been detected in the vadose zone, groundwaters, and mineral deposits collected from the arid southwestern United States, including 155,000 km2 of groundwater in the Southern High Plains (SHP) of Texas and New Mexico. In addition to synthetic sources, natural ClO4- from both Chilean fertilizers and indigenous sources represents a potentially large source of ClO4- in groundwater and drinking water in the United States.