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 90 days of age based on the upper recommended age for DTP1 (2 months or 60 days) plus 30 days late. In a sensitivity analysis, we define delayed vaccination as > 72 days based on the Tanzanian recommended age for the first pentavalent vaccine dose (6 weeks or 42 days) plus 30 days late. Due to the staggered roll-out of the pentavalent vaccine program during the study, we were not able to determine if infants were due for their first DTP vaccination at 4 weeks or 6 weeks and therefore we only present the conservative definition of 72 days late in the sensitivity analysis. Infants who were lost to follow up, died or were vaccinated before 15 days were excluded from the DTP1 analysis. The standard recommended age range for DTP3 vaccination in LMICs was 14 weeks [12 weeks–6 months]) [11, 12]. As a result, we defined delayed DTP3 vaccination as receipt > 210 days (7 months) of age in the main analysis. In a sensitivity analysis, we defined delayed DTP3 vaccination as > 128 days of age based on the Tanzanian recommended age of 14 weeks (98 days) plus 30 days late. Infants who were lost to follow up, died or were vaccinated before 60 days were excluded from the DTP3 analysis. Univariate and multivariate relative risks of delayed or incomplete DTP1 and DTP3 vaccination (> 90 days and > 210 days, respectively) were calculated using log-binomial models stratified by Dar es Salaam and Morogoro region [13]. We also present sensitivity analyses using delayed vaccination definitions of > 72 days and > 128 days for DTP1 and DTP3, respectively. Log-binomial models did not converge in a few instances and in these cases log-Poisson models, which provide consistent but not fully efficient estimates of the relative risk and its confidence intervals, were used [14]. Preterm birth was defined as delivery at < 37 weeks gestation as assessed by maternal report of last menstrual period. Small-for-gestational-age (SGA) was defined, with the use of Oken standards, as birth weight < 10th percentile for gestational age and sex [15]. A wealth index was generated based on household ownership of assets, and households were categorized into wealth quintiles stratified by Dar es Salaam and Morogoro residence [16]. Due to collinearity, low birth weight was modeled separately from preterm birth and small-for-gestational age. P-values for trend in categorical analyses were calculated by treating the median value of each category as a continuous variable. The log-rank test was used to assess the statistical significance of potential effect modification of predictors of interest by study site (Dar es Salaam versus Morogoro). Missing data were retained with use of the missing indicator method. All P values were 2-sided with a P < 0.05 considered statistically significant. All of the analyses for this study were conducted using R version 3.3.1.