Background. Cytotoxin-associated gene A (CagA) product is a bacterial virulence factor contributing to the pathogenicity of Helicobacter pylori (HP) infection in humans. Host factors, which vary in different countries, interact with bacterial factors to determine the disease state. Our objective was to investigate the frequency of CagA-positive HP strains and evaluate the contribution of CagA positivity to symptoms and development of mucosal lesions in HP-infected Turkish children. Methods. We conducted a prospective clinical trial in 240 consecutive Turkish children undergoing endoscopy (110 girls, 130 boys; mean age, 8.7 +/- 4.3 years). HP infection was diagnosed on the basis of a positive rapid urease test and histology of the mucosal specimens. HP IgG and CagA IgG antibodies were measured by enzyme-linked immunosorbent assay in HP-positive children. Results. The HP positivity rate was 50.4% in our study group (51 girls, 70 boys; mean age, 9.9 +/- 3.9 years). CagA was positive in 74.4%. HP infection was less common in children with vomiting (25.9%, P < 0.05). CagA positivity was not associated with any clinical symptom. HP positivity was higher in children with duodenal ulcer (80% vs. 49.1%, P = 0.05); while CagA positivity was similar. Antral nodularity was strongly associated with HP positivity and CagA positivity (30.6% vs. 3.4% and 36.7% vs. 12.9%, respectively, P < 0.05). A negative association between CagA positivity and esophagitis was observed (20% vs. 76.7%, P < 0.05). Conclusions. CagA positivity is common in HP-infected Turkish children. Esophageal lesions are less common in children infected with CagA-positive strains. Although HP is associated with duodenal ulcer disease, CagA positivity does not seem to contribute to development of ulcers in children in our series.