A reliable and sensitive detection of Giardia lamblia cysts, a waterborne pathogenic protozoan parasite, in water sample is important in water supply because they have led to frequent outbreaks of giardiasis in many countries and persist to disinfectants routinely used in drinking water treatment. In this study, the possible options of IMS-PCR procedure for the detection of G. lamblia cysts were compared through the examination of PCR sensitivity between immuno-captured cysts and dissociated cysts after IMS. Immuno-captured or dissociated cysts were freeze-thaw treated in the presence of Chelex-100 prior to PCR. In the case of dissociated samples, the Chelex-100 alleviated PCR inhibition significantly even with small dosage as 5% (w/v) and allowed an outstanding sensitivity of PCR showing DNA amplification for the samples containing 1 cyst. A direct PCR of immuno-captured samples was also possible. However, it showed a less alleviation of inhibition since antibodies and magnetic particles were remaining in PCR mixture and they might have acted as PCR inhibitors.