Aims: Giardia lamblia (G. lamblia) is one of the most common intestinal parasites worldwide. There are some side effects and the reports of parasite resistance to metronidazole as the first line treatment of giardiasis. Therefore, it is essential to discover an effect and safe drug to treat giardiasis. Methodology: In this study, the anti-parasitic activity of hydroalcoholic extracts of Capparis spinosa Linn (C. spinosa) leaves and fruits with different concentrations (4 to 0.125 mg/ml) was assessed against human isolates of the G. lamblia cysts and incubated at 37℃. After staining Giardia cysts with 0.1% eosin, the lethal percentage and 50% lethal concentration (LC50) of fruit and leave C. spinosa L extracts and metronidazole on G. lamblia cysts were calculated after 3, 6, 24 and 48 hours. Results: Anti-giardia activity of fruit and leaf extracts of C. spinosa was different between concentrations and time points (p<0.005). The lethal effect of both C. spinosa L extracts and metronidazole increased significantly in a concentration - and time–dependent response (P<0.0001). The highest lethal percentage of G. lamblia cysts was observed a concentration of 4 mg / ml of fruit (100%) and leaf (44%) extracts of C. spinosa L after 48 hours, respectively. LC50 values were 0.38 ± 0.02mg/ml for fruit extract, 2.32 ± 0.1 mg/ml for leaf extract and 0.53 ± 0.03 µg/ml for metronidazole after 48hours. Conclusion: C. spinosa can be effective in eliminating Giardia cyst of contaminated environments and water.