The current cross-section study aimed to molecular identification of H. pylori directly from gastric tissue biopsies(GTB) and characterize the more frequent vacA genotypes between patients with gastric diseases and their association with disease outcome. Gastric tissue biopsies were collected from 69 patients suffering from symptoms of severe gastro-intestinal tract diseases (GIT), attended to under-went gastro-endoscopy and clinical examination at Gastrointestinal-tract and Liver Disease Hospital, Medical City and Al-Imamein Medical City, Baghdad, Iraq. All patients were subject to the tests included in the current study. Direct identification of H. pylori from GTB and detection of vacA genotypes were done using conventional PCR. The results shown that between 69 gastric patients, 51 (73.9%)were positive for H. pylori. The remaining patients 18/69 (26.1%) were considered as negative control for H. pylori. Among 51 H. pylori positive samples, genotyping of s and m regions of vacA revealed that high frequency of vacA s1b as detected in 22/51 (43.14%) patients and s1a in 17/51 (33.3%) patients. The vacA m2 was detected in 33/51 (64.71%) patients, in compared to vacA m1 which was detected in 15/51 (29.41%) patients. The most frequent vacA allelic combination in patients with GU was s1b/m1 followed by s1a/m1. In conclusion, there was no statistically significant association between vacA genotypes and clinical outcome (?>0.05).