Immunomagnetic separation (IMS) has been specified as a standard method for the measurement of Giardia. In this study, Dynal IMS was evaluated on the basis of recovery efficiencies of Giardia cysts for various IMS operational conditions. The average recoveries for Giardia in deionized, treated and raw water samples were 82.6± 12.2% (n = 6), 75.6± 15.2% (n = 3), and 70.6 ±18.2% (n = 3), respectively. Significant changes in recovery were observed by altering the debris ratio and the debris components of water samples. Changing the reaction volume within the same vessel had no significant effect on cyst recovery efficiencies. However, prolonging the reaction time did increase recovery efficiencies.