Giardia lamblia cysts at low concentrations were detected in water samples using a highly sensitive immunological-PCR (IPCR) method. Magnetic gold particles were precoated with monoclonal anti-Giardia antibodies, and Giardia lamblia cysts ranging from 1 to 100 cysts were diluted in 500 microL of water. A biotinylated detection antibody bound to the G. lamblia cysts was then linked by a streptavidin bridge to biotinylated Giardia-reporter DNA. After extensive washing, reporter DNA was released by denaturation, transferred to PCR tubes, amplified, electrophoresed, and visualized. An optimized immuno-PCR method detected as little as five G. lamblia cysts. To further evaluate the specificity and the clinical application of this IPCR assay for G. lamblia cysts, Entamoeba histolytica and Cryptosporidium parvum were also collected and detected by IPCR. The data demonstrated that this monoclonal antibody-based IPCR method is particularly useful for analysis of environmental water samples in which the densities of G. lamblia cysts is very low, and provides a platform capable of rapid screening of samples from drinking water, wells, rivers, lakes, and recreational swimming pools for trace levels of G. lamblia cysts.