The fate and removal of six selected endocrine disrupting compounds in a lab-scale anaerobic/aerobic (A/O) sequencing batch reactor (SBR), operating at 5 days, solids retention time (SRT) were investigated. A carbamazepine (CBZ), acetaminophen (ATP), diltiazem (DTZ), butyl benzyl phthalate (BBP), estrone and progesterone mix was spiked as model endocrine disrupting compounds (EDC) into domestic wastewater obtained from a nearby sewage treatment plant. The influent, effluent and sludge samples from the SBR unit were analysed by using an LC/MS/MS instrument equipped with electrospray ionization. More than 80% removal was observed for all the EDCs tested. It was found that biodegradation is the most important mechanism for BBP, ATP and progesterone. Biodegradation constants were calculated according to the simplified Monod model for these compounds. The DTZ seemed to have lower rate of biodegradation. The CBZ appeared totally resistant to biodegradation. However, it presented a high rate of sorption onto the sludge and was thereby treated. This contradicts with the literature studies.