Background Limited research has been published on current Helicobacter pylori infection rate in asymptomatic children in China. Aim To assess current Helicobacter pylori infection rate, distribution characteristics and risk factors in Chinese asymptomatic children. Methods A prospective, cross-sectional, population-based study was performed from 2009 to 2011 in three cities of China. Helicobacter pylori infection was diagnosed by a stool antigen test. Multi-stage cluster random sampling was used to select asymptomatic children including neonates. Socioeconomic details were obtained through a standardised questionnaire. Results Among total of 3491 children (0-18 years), the global infection rate was 6.8% and there were no significant differences between genders. Age specific infection rate between regions was significantly different (P < 0.05). The infection rate significantly increased with age (P for trend <0.01). It was low during the newborn (0.6%) to preschool period and was significantly increased in high school students (13.5%) (P < 0.01). Multivariable regression indicated that hand sanitisation, individually served meals, higher education level of mother, above average living space and residence in urban areas were significantly protective against infection (OR 0.749, 0.698, 0.720, 0.838 and 0.770 respectively). Conversely, consuming meals in unsanitised conditions, sharing towels, receiving pre-chewed food from the mother, artificial feeding and family history of gastrointestinal disease were significantly associated with the risk of infection (OR 1.200, 1.965, 2.002, 1.071 and 2.093 respectively). Conclusions Helicobacter pylori infection rate increases with age in Chinese asymptomatic children and is common after 10 years of age. The rate of infection is related to socioeconomic status.