Clinical decision support systems (C-DSS) provide supportive tools to the expert for the determination of the disease. Today, many of the support systems, which have been developed for a better and more accurate diagnosis, have reached a dynamic structure due to artificial intelligence techniques. However, in cases when important diagnosis studies should be performed in secret, a secure communication system is required. In this study, secure communication of a DSS is examined through a developed double layer chaotic communication system. The developed communication system consists of four main parts: random number generator, cascade chaotic calculation layer, PCM, and logical mixer layers. Thanks to this system, important patient data created by DSS will be conveyed to the center through a secure communication line.