Perchlorate anion (ClO4-) is a contaminant of surface and groundwaters in locations throughout the world, primarily as a result of military and industrial activities. Perchlorate has known thyroid activity and has been used as a pharmaceutical to treat hyperthyroidism. Perchlorate, as ammonium perchlorate, is a powerful oxidant used in solid rocket fuels; hence, sources of contamination generally occur near military test sites and chemical manufacturing plants. Perchlorate has also been detected in South American based fertilizers due to natural deposits. Likewise, some perchlorate has been detected in US waters where no known military or industrial activity has taken place. Often these levels are quite low and may not be detectable by traditional analytical methodology. The most commonly used method is EPA 314, which has a reporting limit of 4 mg/L. A novel analytical method has been developed which utilizes liquid chromatography with tandem mass spectrometry (LC/MS/MS) to accurately measure trace (ng/L) levels of the perchlorate anion. This technique is extremely sensitive and selective with a resulting method reporting limit of 0.050 mg/L with only a 10 mL injection volume. This technique can also detect chlorate, iodate, and bromate anions simultaneously with similar sensitivities. Using this new technique, several surface, ground, and bottled waters were analyzed. In some waters previously thought to have no perchlorate contamination, detectable concentrations ranging from 0.050 - >0.300 mg/L were discovered. Several commercially available bottled waters were testing and over 30% contained detectable levels of perchlorate with concentrations ranging from 0.050 - 0.170 mg/L. Additionally, many of these bottled waters were found to contain bromate at levels as great as 80 mg/L. The need for low-level analytical methods is of significant importance considering the EPA draft reference dose for perchlorate of 1 mg/L for drinking water. Furthermore, more sensitive analytical tools provide data necessary for more detailed fate and transport information. Using a slight variation to the drinking water method, this analytical method can also be used for measuring perchlorate in tissue samples. Using this method, it was determined that perchlorate did not appreciably bioconcentrate in the tissues of fish, with resulting bioconcentration factors always less than one. The method described here is robust, rapid, and requires less than one mL of sample volume, and is easily adapted for using with solid matrices such as animal tissues. Includes 26 references, tables.