Background: The global allocation and high level of frequency with the consequence of related pathologies make the eradication of Helicobacter pylori is a very useful advance to test and treat. In addition, the determination of the genotype of H. pylori isolates helps us to comprehend the correlation between assumed virulence genes and clinical disease out come. Objectives: To determine the prevalence of H. pylori infections in patients complaining of gastric disorders, the best phenotypic method for detection of H. pylori and the antimicrobial susceptibility patterns among the isolated strains. To compare between phenotypic and genotypic detection methods and to evaluate the frequency of vacA, cagA and iceA genotypes with their clinical outcomes. Methodology: This study was carried out by collecting gastric biopsy endoscopic specimens from 92 participants admitted to Internal Medicine Endoscopy Unit, Faculty of medicine, Menoufia University. Direct detection of H. pylori in gastric biopsy specimens was done by polymerase chain reaction (ureA gene), microaeroplillic culturing, histological examination and Campylobacter like organism (CLO) rapid urease test. Antimicrobial susceptibility patterns among the isolated strains were determined by disc diffusion method. Some virulence genes (cytotoxin-associated gene (cagA), vaculating cytotoxin (vacA) alleles; vacAs1, vacAs2 and vacAm, also induced by contact epithelium (iceA)) were determined using multiplex PCR. Results: H.pylori genome (UreA) detection by conventional PCR was used as the confirmatory diagnostic tool with 70 PCR positive isolates from 92 participants totally by 76.1%. Histo-pathological examination by both H&E and Giemsa stain detected H. pylori in 68 cases (73.9%). CLO rapid urease test detected H.pylori urease activity in 64 cases (69.6%). Microaerophilic culturing detected H. pylori growth in only 32 cases (34.8%). About 100%, 68.8%, 81.3%, 68.8% and 12.5% of isolates were resistant to metronidazole, amoxicillin, tetracycline, clarithromycin and ciprofloxacin respectively. CagA was identified in 58 isolates (82.9%), iceA in 38 (54.3%), vacAs1 in 22 (31.4%), vacAs2 in 10 (14.3%), vacAm in 32 (45.7%). CagA and cagA+vacAs1m1+IceA were the most prevalent genotypes. Conclusion: Egypt is among the countries that reported high prevalence rate of H.pylori infections mainly with antibiotic resistant virulent strains.