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This paper presents a blind source separation method for convolutive mixtures of speech/audio sources. The method can even be applied to an underdetermined case where there are fewer microphones than sources. The separation operation is performed in the frequency domain and consists of two stages. In the first stage, frequency-domain mixture samples are clustered into each source by an expectation-maximization (EM) algorithm. Since the clustering is performed in a frequency bin-wise manner, the permutation ambiguities of the bin-wise clustered samples should be aligned. This is solved in the second stage by using the probability on how likely each sample belongs to the assigned class. This two-stage structure makes it possible to attain a good separation even under reverberant conditions. Experimental results for separating four speech signals with three microphones under reverberant conditions show the superiority of the new method over existing methods. We also report separation results for a benchmark data set and live recordings of speech mixtures.