BACKGROUND: We determined the risk factors associated with unvaccinated children in rural Gambia. METHODS: We conducted prospective demographic surveillance and recorded immunisations in real time in the Upper River Region, The Gambia. Analysis included residents born from 1 January 2012 to 31 December 2016. Data included age, sex, household members and relationships, migrations, births, deaths, ethnicity, residential location and birth type. Children were defined as unvaccinated at 10, 15 and 24 mo of age if they missed all primary series doses (pentavalent, oral polio and pneumococcal conjugate vaccines), secondary series (first dose measles and yellow fever vaccines) or both vaccination series, respectively. Logistic regressions measured the association between risk factors and being unvaccinated. RESULTS: In total, 5% (1567/30 832) of infants born during the study period and who were residents at the age of 10 mo were unvaccinated. Being unvaccinated at 10 mo of age was associated with children; who did not reside with either parent (adjusted OR 2.26, 95% CI 1.60 to 3.19), whose parents were not the head of household (1.29, 1.09 to 1.52), who had experienced immigration (2.78, 1.52 to 5.08) or who were not of Mandinka ethnicity (between 1.57 and 1.85 for other ethnicities). CONCLUSIONS: Family characteristics are associated with unimmunised children in rural Gambia. Our findings may inform strategies to increase vaccine coverage.