Objectives: To investigate the association between EBV viral infectious dose, infection with EBV and/or H. pylori and histologically different gastric diseases and cancer. Also, to study the association between EBV and/or H. pylori infection with DNA methylation patterns of human tumor suppressor genes p16 and CDH1 in progression of primary gastric diseases to neoplasia. Methods: The current prospective cross-section study included a total of 94 GTPs taken from patients suffering from gastro-duodenal manifestations recruited to Gastro-Endoscopy Department at Gastroenterology and Hepatology Teaching Hospital, Baghdad, Iraq, from November 2017 to October 2018. Two gastric tissue biopsies (GTBs) were collected from those patients. Genomic DNA was extracted from fresh GTPs. Direct molecular identification of H. pylori in extracted DNA was performed by amplification of species-specific urea. Identification of Epstein-Barr nuclear antigen 1(EBNA1) in extracted DNA was performed using nested PCR. DNA samples positive to EBNA1 were submitted for viral load estimation using quantitative real time PCR. Methylation patterns of p16 and CDH1 promoters were detected in modified DNA samples by sodium sulfate using MS-PCR. Results: Of total samples, 39 (41.5%) of DNA samples were positive for H. pylori and 18 (19.15%) DNA samples were positive for EBNA-1. Studying EBV load, 8/23DNA samples were showed infectious dose of EBV. Studying methylation patterns of p16 and CDH-1 promoters, 21/42 and 19/42 DNA samples were provide results for MSPPCR, respectively. Conclusion: Epstein-Barr virus and H. pylori infection may have a synergistic effect in developing different gastric diseases and that enable the clinician to choose the suitable treatment regime.