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Abstract Background Compared to hosting populations, immigrants are usually considered more vulnerable to communicable diseases, many of which are vaccine-preventable. This study aims to estimate vaccination coverage (VC) and timeliness in children born to women from high migratory pressure countries (HMPC) and to evaluate factors affecting differences with children born to Italian women or women from advanced development countries (ITA + ADC). Methods We retrospectively analysed data of children born in 2009–2014 and resident in areas served by three local health units in the cities of Rome (n = 40,284), Turin (n = 49,600), and Treviso (n = 20,080). Data were retrieved through record-linkage of the population, vaccination, and birth registries. We used the Kaplan-Meier method to estimate VCs at different ages for the 3rd dose of vaccine against tetanus and the 1st dose of vaccines against measles and meningococcal group C. Factors affecting differences in VCs by citizenship were evaluated using log-binomial models. Results In Rome, VCs at 2 years of age were consistently higher in children born to ITA + ADC women than in children born to HMPC women, while differences in VCs by citizenship varied according to antigen and birth-cohort in Turin and Treviso, respectively. Where differences were observed, these were only partially explained by the mother's socio-demographic characteristics, level of utilisation of health-services during pregnancy, and maternal, perinatal, and neonatal outcomes. Finally, we observed a reduction of VCs in recent birth cohorts (2012–14 vs. 2009–11), especially in children born to ITA + ADC women. Conclusions Differences in VCs by citizenship were not homogeneous and varied according to geographical context, antigen, and birth-cohort. These differences are likely to be also affected by informal barriers (e.g., linguistic and cultural barriers), which should be addressed in implementing strategies to increase vaccine uptake in foreign children. Moreover, our results suggest that effective strategies to promote vaccinations in the autochthonous population are also needed. [ABSTRACT FROM AUTHOR]