Immunization Information Systems are confidential computerized population-based systems that collect data from vaccination providers on individual vaccinations administered along with limited patient-level characteristics. Through a data use agreement, Centers for Disease Control and Prevention obtains the individual-level data and aggregates the number of vaccinations for geographical statistical areas defined by the US Census Bureau (counties or equivalent statistical entities) for each vaccine included in system. Currently, 599 counties, covering 11 states, collect and report data using a uniform protocol. We combine these data with inter-decennial population counts from the Population Estimates Program in the US Census Bureau and several covariates from a variety of sources to develop model-based estimates for each of the 3,142 counties in 50 states and the District of Columbia and then aggregate to the state and national levels. We use a hierarchical Bayesian model and Markov Chain Monte Carlo methods to obtain draws from the posterior predictive distribution of the vaccination rates. We use posterior predictive checks and cross-validation to assess the goodness of fit and to validate the models. We also compare the model-based estimates to direct estimates from the National Immunization Surveys.