Chronic liver diseases (CLDs) represent an important health issue in developing countries and are commonly associated with impaired immunity. This increases the susceptibility to various infectious agents including parasitic infections, which should be properly managed to avoid life threatening complications. This study assessed the feasibility of rapid, easy and applicable screening test for Giardia and Cryptosporidium within 150 CLDs patients suitable for upper endoscopic examination. Stool samples, duodenal aspirates and duodenal biopsies were examined for G. lamblia and C. parvum by different diagnostic techniques. The results showed stool microscopy (13.3% & 7.3%), duodenal aspirate microscopy (5.3% & 4.7%), rapid lateral flow immune-chromatographic assay (RLFIA) applied on duodenal aspirate samples (16.7% & 10%), duodenal biopsies histopathological examination (6.7% & 5.3%) and direct fluorescent antigen detection in stools (16.7% & 9.3%) for giardiasis and cryptosporidiosis respectively. The high sensitivity of lateral flow immune-chromatographic assay in detecting Giardia and Cryptosporidium in duodenal fluid samples proved a good screening test for these patients.