The occurrence of perchlorate in the Tone River Basin was investigated using an ion chromatograph (IC) coupled with a tandem mass spectrometer (MS/MS). Perchlorate was found at high concentrations in the upper Tone River and its tributary, Usui River, and the maximum concentrations were 340 and 2300 microg/L, respectively. The possible sources of perchlorate in two areas were attributable to industrial effluents. In case of the upper Tone River, perchlorate concentration in an effluent was 1100 microg/L and its concentrations in a tributary (or waterway) directly downstream of the outlet of the effluent ranged from 44 to 1500 microg/L. In case of the Usui River, perchlorate concentration in another effluent was 15,000 microg/L and its concentrations downstream of the outlet of the effluent were 1100-3900 microg/L. Due to the discharge of perchlorate in the upper Tone River Basin, perchlorate concentrations in the river waters of the middle and lower Tone River Basin were generally 10-20 microg/L. Perchlorate concentrations in 30 tap water samples were investigated. Water sources of three tap water samples were other than the Tone River Basin and their perchlorate concentrations were 0.16-0.87 microg/L. On the other hand, water sources of the remaining 27 samples were the upper, middle and lower Tone River Basin and their perchlorate concentrations were 0.06-37 microg/L. Perchlorate concentrations were more than 1 microg/L in 19 tap water samples and more than 10 microg/L in 13 samples. It was shown that tap waters in the Tone River Basin were widely contaminated with perchlorate. To our knowledge, this study was the first to report on perchlorate contamination of environmental and drinking waters in Japan.