Typically, pharmaceutical wastewater is characterized by high chemical oxygen demand (COD) concentration, and some pharmaceutical wastewaters can have COD as high as 1100 mg/L. Due to high organic content, anaerobic technology is a promising alternative for pharmaceutical wastewater treatment. Consequently, in the present study,an anaerobic packed bed reactor was designed and employed to treat highly polluted of pharmaceutical wastewater of Samarra Drug Factory (SDI) in Samarra city (north of Baghdad) in Iraq and suggested to be added to the available wastewater treatment unit of SDI. The efficiency of the anaerobic filter with respect to bed height of filter was studied. The results showed that the first third of filter was the more effective. The filter completed the acclimation period within 34 days in which the COD removal efficiency was 85%. The results also showed that the best hydraulic retention time (HRT) was 24 hours for anaerobic stage and the removal efficiencies of COD and BOD were 87%, 90% for anaerobic stage at the 65th day of operation.