Giardia lamblia a protozoan parasite which causes a severe disease called Giardiasis. G. lamblia is the only species which infects humans, of its7 genotypes, only assemblage A and B are known to cause disease in humans. This study was conducted to determine the prevalence of Giardia cysts in raw wastewater and its prevalence the study community. Furthermore, the prevalence of assemblage A and B in sewage was compared with their prevalence in stool. Wastewater samples of 200 ml were collected from two wastewater plants, Giardia was concentrated and affinity purified by centrifugation and immune magnetic separation and enumerated microscopically by FA. DNA was extracted from the samples and used for genotyping by PCR-RFLP. One mL stool was processes similar to wastewater for microscopic enumeration and genotyping. All wastewater samples were found positive for Giardia at a concentration range of 10-12225 cysts/L. Positive stool samples contained Giardia at average concentration of 1.4x105cysts/ml. In wastewater, 38.2% samples contained assemblage A, whereas assemblage B was not detected separately. However, 61.8% of the samples were found to contain both genotypes. In stool samples a different pattern was observed where the majority (53.8%) were found to contain assemblage B, 34.6% contained assemblage A and only 11.53% contained both assemblage. The results of the study indicate that Giardia is highly prevalent in wastewater in Israel reflecting its prevalence in the community. In addition, assemblage A is highly prevalent in wastewater, whereas assemblage B is more prevalent in stool samples, suggesting milder and carrier state of infection.