Atypical speech productions, regardless of their origins (accents, learning, pathology), need to be assessed with regard to "typical" or "expected" productions. Evaluation is necessarily based on comparisons between linguistic forms produced and linguistic forms expected. In the field of speech disorders, the intelligibility of a patient is evaluated in order to measure the functional impact of his/her pathology on his/her oral communication. The usual method is to transcribe orthographic linguistic forms perceived and to assign a global and imprecise rating based on their correctness or incorrect. To obtain a more precise evaluation of the production deviations, we propose a measurement method based on phonological transcriptions. An algorithm computes automatically and finely the distances between the phonological forms produced and expected from cost matrices based on the differences of features between phonemes. A first test of this method among a large population of healthy speakers and patients treated for cancer of the oral and pharyngeal cavities has proved its validity.