BACKGROUND: Helicobacter pylori infection has been associated with early childhood growth impairment in high- and middle-income countries; however, few studies have examined this relationship within low-income countries or have used a longitudinal design. The possible effects of H. pylori infection on growth trajectories were examined in a cohort of young Ethiopian children. METHODS: In 2011/12, 856 children (85.1% of the 1006 original singletons in a population-based birth cohort) were followed up at age 6.5 years. An interviewer-led questionnaire administered to mothers provided information on demographic and lifestyle variables. Height and weight were measured twice, and the average of the two measurements was used. Exposure to H. pylori infection was assessed using a rapid H. pylori stool antigen test. The independent associations of positive H. pylori infection status (measured at ages 3 and 6.5 years) with baseline height and weight (age 3 years) and height and weight growth trajectory (from age 3 to 6.5 years) were modelled using hierarchical linear models. RESULTS: At baseline (age 3 years), the children's mean height was 85.7cm and their mean weight was 11.9kg. They gained height at a mean rate of 8.7cm/year, and weight at a mean rate of 1.76kg/year. H. pylori infection was associated with lower baseline measurements and linear height trajectory (β=-0.74cm and -0.79cm/year, respectively), after controlling for demographics and markers of socio-economic status. However, the positive coefficient was associated with quadratic growth in height among H. pylori-infected children (β=0.28, 95% confidence interval 0.07 to 0.49, p<0.01), and indicated an increase in height trajectory as the child increased in age. A non-significant difference in baseline and trajectory of weight was observed between H. pylori-infected and non-infected children. CONCLUSIONS: These findings add to the growing body of evidence supporting that H. pylori infection is inversely associated with childhood growth trajectory, after controlling for a range of factors associated with reduced growth and H. pylori status. Further follow-up will be important to confirm possible catch-up in height trajectory among H. pylori-infected children as they grow older.