Based on the rough set theory which is a powerful tool in dealing with vagueness and uncertainty, an algorithm to mine association rules in incomplete information systems was presented and the support and confidence were redefined. The algorithm can mine the association rules with decision attributes directly without processing missing values. Using the incomplete dataset Mushroom from UCI machine learning repository, the new algorithm was compared with the classical association rules mining algorithm based on Apriori from the number of rules extracted, testing accuracy and execution time. The experiment results show that the new algorithm has advantages of short execution time and high accuracy.