Background: Clinical decision support systems (CDSS) are a category of health information technologies that can assist clinicians to choose optimal treatments. These support systems are based on clinical trials and expert knowledge; however, the amount of data available to these systems is limited. For this reason, CDSSs could be significantly improved by using the knowledge obtained by treating patients. This knowledge is mainly contained in patient records, whose usage is restricted due to privacy and confidentiality constraints. Methods: A treatment effectiveness measure, containing valuable information for treatment prescription, was defined and a method to extract this measure from patient records was developed. This method uses an advanced cryptographic technology, known as secure Multiparty Computation (henceforth referred to as MPC), to preserve the privacy of the patient records and the confidentiality of the clinicians' decisions. Results: Our solution enables to compute the effectiveness measure of a treatment based on patient records, while preserving privacy. Moreover, clinicians are not burdened with the computational and communication costs introduced by the privacy-preserving techniques that are used. Our system is able to compute the effectiveness of 100 treatments for a specific patient in less than 24 minutes, querying a database containing 20,000 patient records. Conclusion: This paper presents a novel and efficient clinical decision support system, that harnesses the potential and insights acquired from treatment data, while preserving the privacy of patient records and the confidentiality of clinician decisions.