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Abstract Background Recent trends in global vaccination coverage have shown increases with most countries reaching 90% DTP3 coverage in 2008, although pockets of undervaccination continue to persist in parts of sub-Saharan Africa particularly in the urban slums. The objectives of this study were to determine the vaccination status of children aged between 12-23 months living in two slums of Nairobi and to identify the risk factors associated with incomplete vaccination. Methods The study was carried out as part of a longitudinal Maternal and Child Health study undertaken in Korogocho and Viwandani slums of Nairobi. These slums host the Nairobi Urban Health and Demographic Surveillance System (NUHDSS) run by the African Population and Health Research Centre (APHRC). All women from the NUHDSS area who gave birth since September 2006 were enrolled in the project and administered a questionnaire which asked about the vaccination history of their children. For the purpose of this study, we used data from 1848 children aged 12-23 months who were expected to have received all the WHO-recommended vaccinations. The vaccination details were collected during the first visit about four months after birth with follow-up visits repeated thereafter at four month intervals. Full vaccination was defined as receiving all the basic childhood vaccinations by the end of 24 months of life, whereas up-to-date (UTD) vaccination referred to receipt of BCG, OPV 1-3, DTP 1-3, and measles vaccinations within the first 12 months of life. All vaccination data were obtained from vaccination cards which were sighted during the household visit as well as by recall from mothers. Multivariate models were used to identify the risk factors associated with incomplete vaccination. Results Measles coverage was substantially lower than that for the other vaccines when determined using only vaccination cards or in addition to maternal recall. Up-to-date (UTD) coverage with all vaccinations at 12 months was 41.3% and 51.8% with and without the birth dose of OPV, respectively. Full vaccination coverage (57.5%) was higher than up-to-date coverage (51.8%) at 12 months overall, and in both slum settlements, using data from cards. Multivariate analysis showed that household assets and expenditure, ethnicity, place of delivery, mother's level of education, age and parity were all predictors of full vaccination among children living in the slums. Conclusions The findings show the extent to which children resident in slums are underserved with vaccination and indicate that service delivery of immunization services in the urban slums needs to be reassessed to ensure that all children are reached.