The rejection of cyclophosphamide (CP) by nanofiltration (NF) and reverse osmosis (RO) membranes from ultrapure (Milli-Q) water and membrane bioreactor (MBR) effluent was investigated. Lyophilization-extraction and detection methods were first developed for CP analysis in different water matrices. Experimental results showed that the RO membrane provided excellent rejection (>90%) under all operating conditions. Conversely, efficiency of CP rejection by NF membrane was poor: in the range of 20-40% from Milli-Q water and around 60% from MBR effluent. Trans-membrane pressure, initial CP concentration and ionic strength of the feed solution had almost no effect on CP retention by NF. On the other hand, the water matrix proved to have a great influence: CP rejection rate by NF was clearly enhanced when MBR effluent was used as the background solution. Membrane fouling and interactions between the CP and water matrix appeared to contribute to the higher rejection of CP.