The aim of this paper is to show the system for making a decision in the diagnostics of the patients with autoimmune diseases. In this paper we consider the patients with systemic lupus erythematosus (SLE), Sy Sjogren and systemic sclerosis. In medicine, unlike many other fields, much of the relatively homogeneous and well systematized medical knowledge is implicitly given in the histories of patients. This opens the possibility that medical experts formulate a framework for their knowledge, and those systems based on the effective strategies judgment, produce the useful knowledge from such formulated framework and the adequate history of the illness of the patients. In this research we proposed new distances for the missing values in the cluster optimization. The support system in the diagnostics uses these proposed distances implemented in the program language c#.