In the article a therapy selection method by using topological modelling and multi- objective optimization is presented. In a medicine practice a doctor by taking into the count patients’ health state and laboratory results, tries to suggest a treatment strategy, which mostly is a drug therapy. To solve this task a decision support system has been developed and proposed. The system includes a mathematical model of three self connected diseases. Therapies are evaluated by five efficiency objectives. To find the optimal therapy, seven multi- objective methods are selected and used. Optimization methods form decision support module which is implemented in the medical computer system. To evaluate a performance of the system, test examples are analysed. Conclusion includes the summary and proposals of further research.