The identification and eradication of Helicobacter Pylori (HP) is vital to prevent gastric cancer. After the detection of the HP colonization, accompanying histopathological findings belonging the gastric carcinogenesis should also be considered. According to the widely accepted proofs, although the presence of HP colonization initiates the sequential changes of carcinogenesis, the success rate of the histopathologic diagnosis of HP colonization in the mucosal areas with intestinal metaplasia is controversial. In this study we try to find out the incidence of HP colonization, the relation between HP colonization and gastric intestinal metaplasia (IM) and to describe mucosal pathologic changes. This prospective study was performed between August 2014 and September 2015 in endoscopy unit of Istanbul Traning and Research Hospital after obtaining ethical approve. In total, 201 Turkish patients were included into study. Demography, body mass index, endoscopic findings were enrolled. Fourquadrant biopsy was taken from each patient, including at least 3 pieces from each area. A total of 2412 biopsy material were investigated. All parameters were compared for each grouping method seperatly. No person has completely normal mucosal findings. Prevalence of HP colonization and IM were 82% and 31%. The rate of HP colonization was not significantly different in the areas with or without IM (P = 0.823). IM was detected in at least one biopsy area in 63 (31%) patients, and more common in older patients (P = 0.006). The rate of HP colonization and IM in cardia without simultaneous presence in the other sides of stomach were 3.5% and 2.5%, respectively. Routine biopsy from the cardia may not be required. HP colonization rate was not different between the areas with and without IM. Endoscopic biopsy is still the gold standard for diagnosis of HP colonization, even if IM exists.