Introduction: Helicobacter pylori is a common bacterial infection in humans with early acquisition in childhood. It is adapted to the gastric environment and has been associated with chronic active gastritis, peptic ulcers, atrophic gastritis, gastric adenocarcinoma and mucosa associated lymphoid tissue (MALT) lymphoma. H. pylori strains bearing the Cytotoxin Associated Gene-A (CagA) gene have enhanced pathogenicity and have been strongly linked with increased risk for gastric carcinoma in adulthood. Objectives: The primary objective was to determine the prevalence of CagA positive strains in children with H. pylori infection. The secondary objectives were to compare CagA status and endoscopy findings and to determine their correlation with Iron deficiency in children with H. pylori infection. Methodology: A cross sectional survey was carried out in 73 children under the age of 15 years who had undergone Upper Gastrointestinal (GI) endoscopy and had H. pylori identified on histology. Consent was obtained from the caregivers before administering a questionnaire on bio data and clinical history. Blood samples were drawn and evaluated for anti- CagA IgG antibodies using ELISA to determine prevalence of CagA positive H. pylori infection. Endoscopy findings, iron status as determined by serum ferritin level, haemoglobin level, mean corpuscular volume (MCV) and mean corpuscular haemoglobin (MCH) were compared with CagA status. Data Analysis: Data on age were summarized using median (IQR), categorical data were summarized using frequencies and percentages. Prevalence was determined as proportion with CagA positive H. pylori infection as numerator and all children with H. pylori infection as denominator. The association between CagA and demographic characteristics (gender and age-groups) were determined using Chi square test and logistic regression. Relationship between iron deficiency anaemia and endoscopy findings as exposure variables and CagA status as outcome was analysed. In view of the small sample size, exact logistic regression was used to calculate the odds ratio (OR) and the corresponding confidence interval. Precision was estimated using 95% confidence interval with p-values of ≤0.05 being considered statistically significant. All statistical analyses were done using STATA version 14. Results: Children below the age of 15years (median age of nine years (IQR six to 13) were recruited, 50.7% (n=37) were males. The overall prevalence of CagA was 60.3% (95% CI=48.1% - 71.5%). H. pylori infection was highest in the 5-11 year age group with a prevalence of 59.5% had CagA positive strain. The difference in proportion between the age groups was however not statistically significant (Exact p-value