Perchlorate is an inorganic anion that inhibits iodide transport to the thyroid by sodium-iodide transporters. Because perchlorate is highly soluble, stable, and mobile in water, drinking water is a potential source of perchlorate exposure. When exposed to perchlorate, thyroid dysfunction can be observed in sensitive populations (pregnant woman, infants, and children), especially those with iodide deficiency. The aim of this study was to determine the perchlorate levels in tap water from five cities in Turkey. Perchlorate concentrations of 145 tap water samples collected from Ankara, Isparta, Istanbul, Kayseri, and Sakarya were determined by liquid chromatography-tandem mass spectrometry. Mean and median values were found to be 0.15 and 0.07 mu g/L, respectively. The median values (25-75% percentile) of Istanbul, Ankara, Sakarya, Isparta, and Kayseri were 0.08 mu g/L (0.04-0.09 mu g/L), 0.07 mu g/L (0.07-0.21 mu g/L), 0.04 mu g/L (0.04-0.04 mu g/L), 0.03 mu g/L (0.02-0.07 mu g/L), and 0.25 mu g/L (0.23-0.31 mu g/L), respectively. The median perchlorate level observed in Kayseri was significantly higher than those found at other cities (p < 0.05). Perchlorate concentrations in water samples were lower than the interim drinking water health advisory level (15 mu g/L) determined by the US Environmental Protection Agency. This study showed that perchlorate in drinking water is not the main source of exposure in these cities. Future studies should be performed to determine perchlorate levels in other potential sources, such as food products.