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If the missing values in IISs are not handled properly, they will destroy the internal connection of data and reduce the efficiency of data usage. In this paper, in order to establish effective methods for filling missing values, we propose a new information system, namely, a fuzzy set-valued information system (FSvIS). By means of the similarity measures of fuzzy sets, we obtain several binary relations in FSvISs, and we investigate the relationship among them. This is a foundation for the researches on FSvISs in terms of rough set approach. Then, we provide an algorithm to fill the missing values in IISs with fuzzy set values. In fact, this algorithm can transform an IIS into an FSvIS. Furthermore, we also construct an algorithm to fill the missing values in IISs with set values (or real values). The effectiveness of these algorithms is analyzed. The results showed that the proposed algorithms achieve higher correct rate than traditional algorithms, and they have good stability. 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