A number ofcagPAI genes in theHelicobacter pylorigenome are considered the most evolved genes under a diversifying selection and evolutionary pressure. Among them,cagIandcagNare described as a part of the two different-operon ofcagPAI that are involved in the T4SS machinery, but the definite association of these factors with clinical manifestations is still unclear. A total of 70H. pyloriisolates were obtained from different gastroduodenal patients. All isolates were examined for the presence of primaryH. pylorivirulence genes by PCR analysis. Direct DNA sequence analysis was performed for thecagIandcagNgenes. The results were compared with the reference strain. ThecagI,cagN,cagA,cagL,vacAs1m1,vacAs1m2,vacAs2m2,babA2,sabA, anddupAgenotypes were detected in 80, 91.4, 84, 91.4, 32.8, 42.8, 24.4, 97.1, 84.3, and 84.3% of the total isolates, respectively. The most variable codon usage incagIwas observed at residues 20–25, 55–60, 94, 181–199, 213–221, 241–268, and 319–320, while the most variable codon usage in CagN hypervariable motif (CagNHM) was observed at residues 53 to 63. Sequencing data analysis ofcagNrevealed a hypothetical hexapeptide motif (EAKDEN/K) in residues of 278–283 among sixH. pyloriisolates, which needs further studies to evaluate its putative function. The present study demonstrated a high prevalence ofcagIandcagNgenes among IranianH. pyloriisolates with gastroduodenal diseases. Furthermore, no significant correlation betweencagIandcagNvariants and clinical diseases was observed in the present study. However, all patients had a high prevalence ofcagPAI genes includingcagI,cagN,cagA, andcagL, which indicates more potential role of these genes in disease outcome.