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Objective: The aim of this paper is to present a novel fuzzy classification framework for the automatic extraction of fuzzy rules from labeled numerical data, for the development of efficient medical diagnosis systems. Methods and materials: The proposed methodology focuses on the accuracy and interpretability of the generated knowledge that is produced by an iterative, flexible and meaningful input partitioning mechanism. The generated hierarchical fuzzy rule structure is composed by linguistic; multiple consequent fuzzy rules that considerably affect the model comprehensibility. Results and conclusion: The performance of the proposed method is tested on three medical pattern classification problems and the obtained results are compared against other existing methods. It is shown that the proposed variable input partitioning leads to a flexible decision making framework and fairly accurate results with a small number of rules and a simple, fast and robust training process.