When the historical data are limited, the conditional probabilities associated with the nodes of Bayesian networks are uncertain and can be empirically estimated. Second order estimation methods provide a framework for both estimating the probabilities and quantifying the uncertainty in these estimates. We refer to these cases as uncer tain or second-order Bayesian networks. When such data are complete, i.e., all variable values are observed for each instantiation, the conditional probabilities are known to be Dirichlet-distributed. This paper improves the current state-of-the-art approaches for handling uncertain Bayesian networks by enabling them to learn distributions for their parameters, i.e., conditional probabilities, with incomplete data. We extensively evaluate various methods to learn the posterior of the parameters through the desired and empirically derived strength of confidence bounds for various queries.