We measured six acidic analgesics or anti-inflammatories (aspirin, ibuprofen, naproxen, ketoprofen, fenoprofen, mefenamic acid), two phenolic antiseptics (thymol, triclosan), four amide pharmaceuticals (propyphenazone, crotamiton, carbamazepine, diethyltoluamide), three phenolic endocrine disrupting chemicals (nonylphenol, octylphenol, bisphenol A), and three natural estrogens (17beta-estradiol, estrone, estriol) in 24-h composite samples of influents and secondary effluents collected seasonally from five municipal sewage treatment plants in Tokyo. Aspirin was most abundant in the influent, with an average concentration of 7300 ng/L (n = 16), followed by crotamiton (921 ng/L), ibuprofen (669 ng/L), triclosan (511 ng/L), and diethyltoluamide (503 ng/L). These concentrations were 1 order of magnitude lower than those reported in the USA and Europe. This can be ascribed to lower consumption of the pharmaceuticals in Japan. Aspirin, ibuprofen, and thymol were removed efficiently during primary + secondary treatment (> 90% efficiency). On the other hand, amide-type pharmaceuticals, ketoprofen, and naproxen showed poor removal (< 50% efficiency), which is probably due to their lower hydrophobicity (logKow < 3). Because of the persistence of crotamiton during secondary treatment, crotamiton was most abundant among the target pharmaceuticals in the effluent. This is the first paper to report ubiquitous occurrence of crotamiton, a scabicide, in sewage. Because crotamiton is used worldwide and it is persistent during secondary treatment, it is a promising molecular marker of sewage and secondary effluent.