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Background  Delayed vaccination increases the time infants are at risk for acquiring vaccine-preventable diseases. Factors associated with incomplete vaccination are relatively well characterized in resource-limited settings; however, few studies have assessed immunization timeliness.    Methods  We conducted a prospective cohort study examining Diphtheria-Tetanus-Pertussis (DTP) vaccination timing among newborns enrolled in a Neonatal Vitamin A supplementation trial (NEOVITA) conducted in urban Dar es Salaam ( n  = 11,189) and rural Morogoro Region ( n  = 19,767), Tanzania. We used log-binomial models to assess the relationship of demographic, socioeconomic, healthcare access, and birth characteristics with late or incomplete DTP1 and DTP3 immunization.    Results  The proportion of infants with either delayed or incomplete vaccination was similar in Dar es Salaam (DTP1 11.5% and DTP3 16.0%) and Morogoro (DTP1 9.2% and DTP3 17.3%); however, the determinants of delayed or incomplete vaccination as well as their magnitude of association differed by setting. Both maternal and paternal education were more strongly associated with vaccination status in rural Morogoro region as compared to Dar es Salaam ( p -values for heterogeneity < 0.05). Infants in Morogoro who had fathers and mothers with no education had 36% (95% CI: 22–52%) and 22% (95% CI: 10–34%) increased risk of delayed or incomplete DTP3 vaccination as compared to those with primary school education, respectively. In Dar es Salaam, mothers who attended their first antenatal care (ANC) visit in the 3rd trimester had 1.55 (95% CI: 1.36–1.78) times the risk of delayed or not received vaccination as compared to those with a 2nd trimester booking, while there was no relationship in Morogoro. In rural Morogoro, infants born at home had 17% (95% CI: 8–27%) increased risk for delayed or no receipt of DTP3 vaccination. In both settings, younger maternal age and poorer households were at increased risk for delayed or incomplete vaccination.    Conclusion  We found some risk factors for delayed and incomplete vaccination were shared between urban and rural Tanzania; however, we found several context-specific risk factors as well as determinants that differed in their magnitude of risk between contexts. Immunization programs should be tailored to address context-specific barriers and enablers to improve timely and complete vaccination.    Electronic supplementary material  The online version of this article (10.1186/s12879-019-3828-3) contains supplementary material, which is available to authorized users.

Determinants of delayed or incomplete diphtheria-tetanus-pertussis vaccination in parallel urban and rural birth cohorts of 30,956 infants in Tanzania