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Introduction: The aim of the study was to determine the evolutionary role of the Cag A presence in the outcome of eradication treatment of H. pylori. Materials and methods: Sixty-seven pediatric dyspeptic patients (mean age 13.7 years, range 5 to 17 years, male/female 24/43) underwent endoscopy for H.pylori presence. Gastric biopsy specimens were taken for histology and/or culture and one biopsy sample was used for CagA PCR determination. H. pylori positive patients were treated for 2 weeks by amoxycilline (50 mg/kg/day), bismuth subcitrate (8 mg/kg/day), nifuratel (30 mg/kg/day) plus omeprazole (1 mg/kg, once daily). Results: Forty one of 67 children (61.2%) were H. pylori positive. Nineteen of 41 strains (46.3%) were CagA positive and 22 were CagA negative (53.7%). H. pylori was eradicated in 33 patients (80.4%). Among the patients with successful eradication 18 children were CagA positive, fourteen were CagA negative. Thus, more patients with CagA-negative status had evidence of ongoing H. pylori infection (36.4% (8/22) versus 5.3% (1/19); χ2=4.08, p=0.0021; Fisher’s exact test p= 0.0238). Conclusion: In our study the carriage of CagA-lacking strain was associated with failure of treatment. In our opinion, this phenomenon, related to extraordinary genome plasticity, not only allows the microbe to maintain balanced relationship with the host, but also to survive in antibacterial therapy conditions.