ABSTRACT Objective The aim of this study was to prospectively follow a cohort of children without Helicobacter pylori infection and to compare growth velocity in the children who become infected during follow‐up with that of children who remained infection‐free. Methods Three hundred forty‐seven children in general good health, aged 12 to 60 months, who tested negative for H. pylori by the 13 C‐urea breath test, from three daycare centers in a lower‐middle class borough of Cali, Colombia, were monitored for 2.5 years. Anthropometric measurements were performed every 2 months and breath tests every 4 months. Linear mixed models were used to analyze growth velocity in relation to onset of H. pylori infection. Results One hundred five (30.3%) children who were uninfected at the start of the study became infected during follow‐up. Growth velocity in infected children was reduced by 0.042 ± 0.014 cm/mo ( P = 0.003) (approximately 0.5 cm/yr) after adjusting for age. The rate of deceleration in growth velocity was relatively constant over time. Conclusions Among these lower‐middle class children aged 12 to 60 months from a population with high prevalence of H. pylori infection, a new and sustained infection was followed by significant growth retardation.