BACKGROUND: Disease diagnosis is complicated since patients may demonstrate similar symptoms but physician may diagnose different diseases. There are a few number of investigations aimed to create a fuzzy expert system, as a computer aided system for disease diagnosis. METHODS: In this research, a cross-sectional descriptive study conducted in a kidney clinic in Tehran, Iran in 2012. Medical diagnosis fuzzy rules applied, and a set of symptoms related to the set of considered diseases defined. The input case to be diagnosed defined by assigning a fuzzy value to each symptom and then three physicians asked about each suspected diseases. Then comments of those three physicians summarized for each disease. The fuzzy inference applied to obtain a decision fuzzy set for each disease, and crisp decision values attained to determine the certainty of existence for each disease. RESULTS: Results indicated that, in the diagnosis of seven cases of kidney disease by examining 21 indicators using fuzzy expert system, kidney stone disease with 63% certainty was the most probable, renal tubular was at the lowest level with 15%, and other kidney diseases were at the other levels. The most remarkable finding of this study was that results of kidney disease diagnosis (e.g., kidney stone) via fuzzy expert system were fully compatible with those of kidney physicians. CONCLUSION: The proposed fuzzy expert system is a valid, reliable, and flexible instrument to diagnose several typical input cases. The developed system decreases the effort of initial physical checking and manual feeding of input symptoms.