Ammonium perchlorate, a key ingredient in solid rocket propellants, has been found in ground and surface waters in a number of U.S. states, and perchlorate contamination of public drinking water wells is now a serious problem in California. Perchlorate poses a health risk and preliminary data from the U.S. EPA reports that exposure to less than 4-18 microg/l provides adequate human health protection. An improved ion chromatographic method was developed for the determination of low microg/l levels of perchlorate in ground and drinking waters based on a Dionex IonPac AS16 column, an hydroxide eluent generated using an EG40 automated eluent generator, large loop (1000 microl) injection, and suppressed conductivity detection. The method is free of interferences from common inorganic anions, linear over the range of 2-100 microg/l perchlorate, and quantitative recoveries are obtained for low microg/l levels of perchlorate in spiked ground and drinking water samples. The MDL of 150 ng/l permits quantification of perchlorate below the levels that ensure adequate health protection.