Clinical Decision Support Systems (DSS) help improve health care quality. They usually incorporate an Execution Engine (EE), defined for each disease. We have designed, and present here, a generic execution engine, coupled with guideline-based disease specific rules stored in knowledge base (KB) as part of the prescription-critiquing mode of the ASTI project. This system was designed using two national guidelines for type 2 diabetes and hypertension. It takes into account the patient's clinical data, the tolerance and effectiveness of previous and current treatments and the physician's prescription made at the time. The functioning of the system has been speeded up and its maintenance made easier by indexing the KB rules according to the type of treatment they are linked to (e.g. monotherapy, etc.) and by classifying them into four categories. The EE's design formalizes generic therapeutic algorithms, leading to treatment options for cases of bad tolerance or insufficient effectiveness of the current treatment. Its applicability to other diseases was shown by applying it to dyslipidemia.