The environmental estrogens have been well known as a risk for ecosystem and human health. Many natural and man-made estrogens are found in the water environment. However, some unknown estrogenic disinfection byproducts (DBPs) form during the water treatment process, which could escape the water quality monitoring due to the unawareness of their existence. This study developed an estrogen receptor based affinity chromatography to screening unknown estrogenic DBPs from environmental estrogens, 17β-estradiol (E2) and diethylstilbestrol (DES). A strong estrogenic compound (stronger than estrone), Δ9(11)-dehydro-estradiol, was found as a DBP of E2 after chlorine or UV or chlorine-UV combined disinfection. For DES, UV disinfection could cause photochromism, and further dehydrogenation, and generate a strong estrogenic DBP, 9,10-diethylphenanthrene-3,6-diol, which is stronger than E2. This result explains why DES still can persist for a long time in the surface water. While under the oxidative disinfection, like chlorination and ozonation, DES generated a relatively weak estrogen, Z,Z-dienestrol (DE), but it is still stronger than bisphenol A (BPA). In summary, this study proposed a novel way to study the unknown estrogenic DBPs, which might be the potential micropollutants in the water environment.