A method and apparatus are provided for using the uncertainty of a noise-removal process during pattern recognition. In particular, noise is removed from a representation of a portion of a noisy signal to produce a representation of a cleaned signal. In the meantime, an uncertainty associated with the noise removal is computed and is used with the representation of the cleaned signal to modify a probability for a phonetic state in the recognition system. In particular embodiments, the uncertainty is used to modify a probability distribution, by increasing the variance in each Gaussian distribution by the amount equal to the estimated variance of the cleaned signal, which is used in decoding the phonetic state sequence in a pattern recognition task.