Adsorbable organic halogens (AOX) are a general indicator for the total amount of compounds containing organically bonded halogens. AOX concentrations and components were investigated along the wastewater treatment process in four large-scale pharmaceutical factories of China, and genotoxicity based on the SOS/umu test was also evaluated. The results showed that AOX concentrations in wastewater of four factories ranged from 4.6 to 619.4mg/L, which were high but greatly different owing to differences in the raw materials and products. The wastewater treatment process removed 50.0%-89.9% of AOX, leaving 1.3-302.5mg/L AOX in the effluents. Genotoxicity levels ranged between 2.1 and 68.0μg 4-NQO/L in the raw wastewater and decreased to 1.2-41.2μg 4-NQO/L in the effluents of the wastewater treatment plants (WWTPs). One of the main products of factory I, ciprofloxacin, was identified as the predominant contributor to its genotoxicity. However, for the other three factories, no significant relationship was observed between genotoxicity and detected AOX compounds.