The estimation of a meaningful affinity graph has become a crucial task for representation of data, since the underlying structure is not readily available in many applications. In this paper, a topology inference framework, called Bayesian Topology Learning, is proposed to estimate the underlying graph topology from a given set of noisy measurements of signals. It is assumed that the graph signals are generated from Gaussian Markov Random Field processes. First, using a factor analysis model, the noisy measured data is represented in a latent space and its posterior probability density function is found. Thereafter, by utilizing the minimum mean square error estimator and the Expectation Maximization (EM) procedure, a filter is proposed to recover the signal from noisy measurements and an optimization problem is formulated to estimate the underlying graph topology. The experimental results show that the proposed method has better performance when compared to the current state-of-the-art algorithms with different performance measures.