Embryo selection is a critical step in assisted reproduction (ART): a good selection criteria is expected to increase the probability of inducing pregnancy. In the past, machine learning methods have been used to predict implantation and to rank the most promising embryos. Here, we study the use of a probabilistic graphical model that assumes independence between embryos’ individual features and cycles characteristics. It also accounts for a third source of uncertainty attributed to unknown factors. We present an empirical validation and analysis of the behavior of the model within real data. The dataset describes 604 consecutive ART cycles carried out at Hospital Donostia (Spain), where embryo selection was performed following the Spanish Association for Reproduction Biology Studies (ASEBIR) protocol, based on morphological features. The performance of our model is evaluated with different metrics and the predicted probability densities are examined to obtain significant insights about the process. Special attention is given to the relation between the model and the ASEBIR protocol. We validate our model by showing that its predictions show correlation with the ASEBIR score when the score is not provided as a feature. However, once the selection based on this protocol has taken place, our model is unable to separate implanted and failed embryos when only embryo individual features are used. From here, we can conclude that ASEBIR score provides a good summary of morphological features.