The continuous rise in the number of patients suffering from Helicobacter pylori is probably due to the changes in modern life. Nowadays patients suffering from gastrointestinal problems are diagnosed through invasive and noninvasive techniques. The choice of a diagnostic test is influenced by factors such as the tests' sensitivity and specificity, the clinical conditions, and the cost-effectiveness of the testing strategy. This study aimed to compare molecular detection methods of H. pylori by polymerase chain reaction (PCR) targeting the 16S rRNA, ureA and glmM genes with an invasive histopathological technique. A total of 290 patients from various hospitals in Khartoum State were recruited in this study between March 2018 and January 2020. Two gastric biopsies were collected from each patient for PCR and histopathology.A total of 103 (35.5%) samples were positive by histopathological examination, 88 (30.3%) by 16SrRNA, 39 (13.4%) by glmM gene, and 56 (19.3%) by ureA gene. The highest sensitivity was observed in 16SrRNA (46.6%), followed by ureA (35%), and glmM (24.3%). While the best specificity was observed in glmM gene (92.5%), followed by ureA (89.3%) and 16SrRNA (78.6%). In conclusion, the PCR test targeting the16SrRNA gene exhibited the best results for molecular detection of H. pylori compared to other genes.