This paper presents and evaluates an approach to Bayesian model averaging where the models are Bayesian nets (BNs). Prior distributions are defined using stochastic logic programs and the MCMC Metropolis-Hastings algorithm is used to (approximately) sample from the posterior. Experiments using data generated from known BNs have been conducted to evaluate the method. The experiments used 6 different BNs and varied: the structural prior, the parameter prior, the Metropolis-Hasting proposal and the data size. Each experiment was repeated three times with different random seeds to test the robustness of the MCMC-produced results. Our results show that with effective priors (i) robust results are produced and (ii) informative priors improve results significantly.