This paper studies the parameter estimation of a general multi-input, multi-output multi-rate system in the frequency-domain. Two methods, named dividing to subsystems and input extension, are introduced for dealing with multi-rate systems and the later method is easily used to convert a multi-input, multi-output multi-rate system to several sub-problems with fast input updating and slow output sampling. Then all the frequency-domain parameter estimation methods can be applied. Here a least-square parameter estimation method is generalized for parameter estimation in the multi-input, multi-output case. Several examples, including one with real industrial data, are given to show the effectiveness of the methods proposed. (c) 2006 Elsevier Ltd. All rights reserved.