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Abstract: Background: Timely vaccination is important to protect children from common infectious diseases. We assessed vaccination timeliness and vaccination coverage as well as coverage of vitamin A supplementation in a Ugandan setting. Methods and findings: This study used vaccination information gathered during a cluster-randomized trial promoting exclusive breastfeeding in Eastern Uganda between 2006 and 2008 (ClinicalTrials.gov no. NCT00397150). Five visits were carried out from birth up to 2 years of age (median follow-up time 1.5 years), and 765 children were included in the analysis. We used Kaplan–Meier time-to-event analysis to describe vaccination coverage and timeliness. Vaccination coverage at the end of follow-up was above 90% for all vaccines assessed individually that were part of the Expanded Program on Immunization (EPI), except for the measles vaccine which had 80% coverage (95%CI 76–83). In total, 75% (95%CI 71–79) had received all the recommended vaccines at the end of follow-up. Timely vaccination according to the recommendations of the Ugandan EPI was less common, ranging from 56% for the measles vaccine (95%CI 54–57) to 89% for the Bacillus Calmette–Guérin (BCG) vaccine (95%CI 86–91). Only 18% of the children received all vaccines within the recommended time ranges (95%CI 15–22). The children of mothers with higher education had more timely vaccination. The coverage for vitamin A supplementation at end of follow-up was 84% (95%CI 81–87). Conclusions: Vaccination coverage was reasonably high, but often not timely. Many children were unprotected for several months despite being vaccinated at the end of follow-up. There is a need for continued efforts to optimise vaccination timeliness. [Copyright &y& Elsevier]