There are conflicting reports regarding the association of Helicobacter pylori (H. pylori) infection with growth failure. We evaluated the role of H. pylori infection on malnutrition and growth failure in dyspeptic children. The study cases included 108 dyspeptic children and were evaluated by endoscopic gastric biopsy, while 50 healthy children constituted the control group. The study cases were grouped as H. pylori [+] (n = 57) and H. pylori [-] (n = 51) by the presence or absence of microorganism in gastric tissue, respectively. Age, gender, height for age (H/A), weight for height (W/H), body mass index (BMI), weight and height z scores and the daily calorie intake of the children were recorded. Malnutrition and growth failure were evaluated by the Waterlow criteria and height z score, respectively. Then, the H. pylori [+], H. pylori [-] and control groups were compared in relation to the variables defined above. All groups were similar with respect to gender and age. The daily calorie intake was lower in dyspeptic children. Although anthropometric variables were similar in the H. pylori [+] and [-] groups, the control cases had higher W/H compared to both H. pylori [+] (p = 0.030) and H. pylori [-] (p = 0.000) cases, and higher BMI (p = 0.001) and weight z scores (p = 0.014) than those in the H. pylori [-] group. The malnutrition rate was similar in the H. pylori [+] and [-] groups. However, mild acute (p = 0.033) and general malnutrition rates (p = 0.000) were lower in the control cases compared to the study cases. The short stature rate was not different significantly in all three groups. In conclusion, the results of this study do not support the data that H. pylori infection plays an extra role in malnutrition and growth failure in children presenting with dyspeptic complaints. However, as a major cause of dyspepsia, H. pylori infection might be considered to cause malnutrition secondary to decreased calorie intake associated with dyspepsia.