This investigation was carried out during 2011–2012 season at the biotechnology department\General Commission for Scientific Agricultural Researches in order to detect the presence of Giardia Cysts on fresh vegetables and irrigation water using PCR technique to detect the status of Giardia cysts in ten different agricultural areas of Damascus Countryside. 120 samples including, 40 irrigation water and 80 vegetables samples were randomly collected and tested. Out of 120 samples examined, only 25.8 % were contaminated with Giardia cysts and these included 37.5% of irrigation water samples and 20% of fresh vegetables samples. G. lamblia cysts were detected in 12.5% of examined samples, 17.5% of irrigation water samples and 10% of fresh vegetables samples. The majority of contaminated samples (41.6%), (25%) for Giardia and G. lamblia, respectively were from Misraba area without statistically significant with Kafrein area, which showed the lowest contamination with Giardia cysts (8.33%) and was free of G. lamblia cysts. This study confirmed the importance of application of molecular biology methods in the detection of Giardia on vegetables and their Irrigation water, since used primers showed high specificity and sensitivity in the detection of the Giardia genus and discriminate the Human pathogenic type, G. lamblia.