Despite the great emphasis that the medical community has dedicated to clinical practice guidelines in the last few decades, it has become clear that it is difficult to adequately distribute texts (paper-based guidelines) and for them to be used by final users. The reasons for this are manifold: the large number of guidelines delivered each year, their necessary updates on the face of new scientific evidence, the text is not always free from ambiguities, etc. When these problems became evident, the medical informatics community hypothesised that more formal electronic versions would increase the probability of the effective diffusion of guidelines and also physicians' compliance to them. This claim was based on a few hypotheses: one is that formal models, such as flowcharts or other graphical metaphors, provide a more friendly and immediate way of reading a guideline, thus improving learning and absorbing of the guideline content (e. g. using formal models as educational/simulation tools); another hypothesis is that formal models allow easier guideline integration with the daily clinical workflow, raising the possibility of building real-time decision support systems, which again should improve physicians' compliance. This paper focuses on the issues that must be taken into account when modelling guidelines to ensure their effective implementation in real-world computerised environments.