This study was undertaken to investigate the removal of pathogenic microorganisms and their indicators in a laboratory scale biological treatment system that simulated the secondary treatment process of a wastewater treatment plant (WWTP). Four groups of microorganisms including bacteria, viruses, protozoa and helminths as well as the selected indicators were employed in the investigation. The results demonstrated that approximately 2-3 log10 removal of the microbial indicators was achieved in the treatment process. The log removal of Clostridium perfringens spores was low due to their irreversible adsorption to sludge flocs. The laboratory treatment system demonstrated a similar removal capability for Escherichia coli and the bacterial indicators (total coliforms, enterococci and particles <2.73 microm/L). The MS-2 bacteriophage, measured as a viral indicator, showed a lower removal than poliovirus, which may be considered as a worst case scenario for virus removal. The results of using particle profiling as an indicator for protozoa and helminths appeared to be inaccurate. The removal performance for bacterial and protozoan pathogens and their indicators in a full scale WWTP and the laboratory treatment system was compared.