Residual pharmaceutical products in sewage and other water environments have recently become a serious social problem in advanced countries. Among these pharmaceutical products, antibiotics have attracted special attention due to their serious impact on the ecosystem and connections to the emergence of drug-resistant bacteria. Our research intended to develop a new method to analyse the three antibiotics estimated to be released out of the body in large amounts in Japan; levofloxacin (LVFX), clarithromycin (CAM) and azithromycin (AZM), and survey the state of pollution in the sewerage. The concentrations of the water-phase antibiotics LVFX, CAM and AZM were measured in each process of activated sludge process in six wastewater treatment plants. Liquid chromatography tandem mass spectrometry (LC/MS/MS) was used to analyse solutions of the antibiotics after pretreatment with a solid phase extraction. The limits of quantification and the average recoveries for these antibiotics in the influent were 1.2 to 29 ng/L and 46 to 93%, respectively. In the influent, LVFX, CAM and AZM were detected at concentrations of 552, 647 and 260 ng/L, respectively, while their removal efficiencies were 42, 43 and 49%, respectively. Although the CAM and AZM concentrations decreased as the treatment progressed, it was shown that the LVFX concentration increased in activated sludge reactors in some cases. Despite differences in octanol-water partition coefficients among LVFX, CAM and AZM, their removal efficiency showed no major difference. This indicates that this removal phenomenon cannot be explained by simple adsorption by the activated sludge.