Childhood Immunization has been identified as the most cost-effective health intervention in the last century. It is estimated to save more than two millions lives annually. Completion, timeliness and sequencing of routine vaccination as recommended by the World Health Organization is very crucial for maximum protection of children against specific infections. Existence of non-specific effects-effects other than prevention of specific infection–have been documented and could be linked to vaccination timeliness and sequencing. The objective of the study was to determine the prevalence and determinants of vaccination coverage and delays among children aged 12-23 months and establish the relationship with subsequent morbidity, anthropometry and,mortalityin two Nairobi informal settlements.The study targeted households with children aged 12-23 months. Data from the Maternal and Child Health longitudinal study run by Nairobi Health and Demographic Surveillance System and collected between 2007 and 2014 was used. Structured data collection tools were used to collect data from mothers or guardians with children aged between 12 and 23 months. Proportions and medians were used to determine vaccination coverage and levels of delays respectively. Logistic regression models were used to identify determinants of full immunization and delays. Cox regression and Generalized Estimation Equation models were used to assess relationship between immunization patterns and morbidity, anthropometry and mortality respectively. The findings indicated that67% of the children were fully immunized and 22%received their vaccinations out-of-sequence. Mother's education level, post-natal care, and health facility delivery were identified as the determinants of being fully immunized. Place of delivery was identified as the determinant of out-of-sequence. A significant 58% (p=0.017) and 64% (p<0.001) decreases in child mortality was observed for being fully immunized and immunized in recommended sequence respectively. A non-significant 35% (p=0.159) reduction in hospitalization cases was observed for being fully immunized. Vaccine completion was significantly associated with 0.13 (p=0.002) and 0.12 (p=0.006) increase in weight-for-age and weight-for-height z-scores respectively. More focus is needed on making sure all children are immunized on time and as per schedule. The low immunization coverage and age-specific vaccination can easily be improved by targeting disadvantaged groups. Particularattention is needed on the uptake of the measles and the third doses of polio and pentavalent vaccines. Further research is needed to determine the effects of each routine vaccine other than preventing the specific infection.