Eradication of H. pylori by gastric acid inhibition in combination with antibiotics can result in overgrowth of non-H. pylori bacterial flora. This may confound the detection of H. pylori. To assess the intragastric bacterial flora, in 18 patients treated with amoxycillin (2 weeks) and omeprazole (6 weeks), gastric juice was cultured and two biopsies each of duodenum, antrum and corpus were obtained before and at the end of eradication therapy for culture and for histology by modified Giemsa (MG) and immunohistochemistry (IMM) against H. pylori, respectively. Numbers of patients with H. pylori-positive and non-H. pylori positive biopsies by each method are shown in the table. Culture showed a significant increase in amount of oral flora (p < 0.05) in gastric juice, duodenal, antral and body mucosa after therapy. After therapy with culture as standard, sensitivity and specificity of MG were 60.7 and 80.9%, and of IMM 80.3 and 89.4%, respectively.Conclusion: IMM is superior to MG for the detection ofH. pylori . Because of the possible presence of non-H. pylori flora after eradication therapy the use of IMM is recommended in this situation.