The management of business processes can support efficiency improvements in organizations. One of the most interesting problems is the mining and representation of process models in a declarative language. Various recently proposed knowledge-based languages showed advantages over graph-based procedural notations. Moreover, rapid changes of the environment require organizations to check how compliant are new process instances with the deployed models. We present a Statistical Relational Learning approach to Workflow Mining that takes into account both flexibility and uncertainty in real environments. It performs automatic discovery of process models expressed in a probabilistic logic. It uses the existing DPML algorithm for extracting first-order logic constraints from process logs. The constraints are then translated into Markov Logic to learn their weights. Inference on the resulting Markov Logic model allows a probabilistic classification of test traces, by assigning them the probability of being compliant to the model. We applied this approach to three datasets and compared it with DPML alone, five Petri net- and EPC-based process mining algorithms and Tilde. The technique is able to better classify new execution traces, showing higher accuracy and areas under the PR/ROC curves in most cases.