Helicobacter pylori (H.pylori) was identified in human gastric and liver tissues by PCR and partial DNA sequencing. The aim of this work, is to find a relationship between H.pylori infection, chronic liver disease and hepatic encephalopathy (HE) Also, this work aims to find the most sensitive diagnostic method for H.pylori infection. Serum samples were colleted from patients (n=30) and control subjects (n= 20) for diagnosis of HP IgG by chemiluminescence technique. Antral gastric biopsies (n=30) and guided needle liver biopsies from the same patients (n=18) were obtained for diagnosis of H.pylori by PCR. The patients were cirrhotic with past or recent history of HE with or without hospital admission. They were followed up in the Endoscopy Unit of the Internal Medicine Departement, Kasr El Aini hospital. The control subjects were subjected only to serum diagnosis of Hp IgG due to difficulty in obtaining normal gastric and liver tissues. Gastric samples from cirrhotic patients were positive by PCR using H.pylori specific primers for ure C (n=13) and ure A (n=23). Nine patients, were positive for both ure C and ure A primers. Liver samples from cirrhotic patients were positive by PCR using specific primer for H.pylori ure A (n=18) and H.hepaticus ure AB (n=14). Conclusion: Serological diagnosis may not be a sensitive diagnostic method due to the similarity of results between patients and control subjects. The detection of H.pylori in gastric tissue and the same strain in liver tissue may be an indicator of the possible pathogenic role of H.pylori in aggravation of HE symptoms due to H.pylori urease production, which causes more ammonia generation, resulting in increase of neurological symptoms of HE patients. Complete eradication of H.pylori may minimize symptoms of HE and increase patients life span.