BACKGROUND Helicobacter pylori (H.pylori), the main cause of gastric and duodenal ulcer, is considered as a type 1 carcinogen. The primary prevention of gastric cancer is eradicating chronic H.pylori infection. However, the antimicrobial eradication rates are decreasing as low as 80% in some countries, less than 70% in Europe and are inversely correlated with antibiotic resistance rates reported worldwide. The current international guidelines recommended several regimens with higher success rate including sequential, combined, bismuth-containing and resistance-guided treatment and states that the local susceptibility testing in H.pylori should be studied. The research data that is covering correlation between H.pylori associated gastric changes and precancerous diseases, evaluation of H.pylori eradication rate are sparse in Mongolia. METHODS Totally, 495 eligible candidates were enrolled into this study. 225 patients who visited to endoscopy unit, received gastroscopy with multiple biopsies for rapid urease test, histology and H.pylori culturing. Out of these, 131 (52.2%) patients were positive for H.pylori infection. These were further tested for antibiotic resistance. 76 patients were treated with targeted therapy based on antibiotic resistance testing. Another 270 eligible patients with confirmed H.pylori associated gastritis were randomized into the following 1st line therapy regimen groups clarithromycin-based triple therapy (CBTT, n=90); bismuth-based quadruple therapy (BBQT, n=90) and sequential therapy (ST, n=90). In 43 patients that were not responded to 1st line therapy, levofloxacin-based triple therapy (LBTT) was prescribed as a second line treatment. Eradication rates were assessed using H.pylori stool antigen test 28 days of therapy just subsequent to termination of treatment. RESULTS During the gastroscopy, presence of active gastritis, nodular change and atrophy were 32.9%, 12% and 52.9% respectively. Epigastric pain was reported in 73.3%, 62.2%, 60-80% and 41.3% of patients with normal mucosa, nodular change, stomach and duodenal ulcer and antral atrophy (p<0.05). Abdominal fullness was more common among patients with extensive gastric atrophy (69.2%, p<0.05). In <40 age group gastritis was predominantly in the prepylori, while in the >50 age group it was predominantly the corpus region. H.pylori resistance rates to amoxicillin, clarithromycin, metronidazole and more than 2 antibiotics were 8.4%, 37.4%, 74% and 30.5%. On ITT analysis, eradication rates of 1st line H.pylori targeted treatment, CBTT, BBQT and ST were 92.1%, 71.1%, 87.8% and 67.8% (p<0.0001); on PP analysis, that were 94.6%, 72.7%, 89.8% and 68.5% (p<0.0001) respectively. Eradication rates of 2nd line treatment LBTT were 55.8% and 60% by ITT and PP analysis. Higher side-effects were reported during the second line treatment. CONCLUSION H.pylori infection rate was high among the dyspeptic patients resulting chronic gastritis and atrophic change. H.pylori resistance rate to metronidazole and clarithromycin was high. Among 1st line therapies; the eradication rates of CBTT and ST were poor, while BBQT and Targeted therapy had a higher success rate. 2nd line therapy showed higher failure rate.