We have developed a superconducting high gradient magnetic separation (HGMS) system to remove endocrine disrupters from water. The system purified 70 liters of endocrine disrupter polluted water within about several tens of minutes without generating any secondary waste. The system consists of pretreatment processes to form magnetized compounds with endocrine disrupters, and an HGMS device to extract them by using a strong magnetic force from water. We fabricated a novel adsorbent made of micron-sized ferric oxide particles which are not only magnetic but also hydrophobic. Because some of endocrine disrupters are hydrophobic as well, the ferric oxide particles adsorb endocrine disrupters eluted in water according to a hydrophobic interaction. We have succeeded in decreasing the bisphenol A concentrations in fortified water from 69 ng l−1 to 16 ng l−1 and nonylphenol from 7.0 mg l−1 to 0.9 mg l−1. Furthermore, we have successfully demonstrated that we could regenerate the ferric oxide particles, and that they were reusable for the adsorption of endocrine disrupters in water.