In this paper, we propose a new mask estimation method for the computational auditory scene analysis (CASA) of speech using two microphones. The proposed method is based on a hidden Markov model (HMM) in order to incorporate an observation that the mask information should be correlated over contiguous analysis frames. In other words, HMM is used to estimate the mask information represented as the interaural time difference (ITD) and the interaural level difference (ILD) of two channel signals, and the estimated mask information is finally employed in the separation of desired speech from noisy speech. To show the effectiveness of the proposed mask estimation, we then compare the performance of the proposed method with that of a Gaussian kernel-based estimation method in terms of the performance of speech recognition. As a result, the proposed HMM-based mask estimation method provided an average word error rate reduction of 61.4% when compared with the Gaussian kernel-based mask estimation method.