A computer-based system generates alternative phonetic transcriptions for a target word or phrase corresponding to specific phonological processes that replace individual phonemes or clusters of two or more phonemes with replacement phonemes. The system compares a user's speech with a list of possible transcriptions that includes the base (i.e., correct) transcription of the test target as well as the different alternative transcriptions, to identify the transcription that best matches the user's. In a speech therapy application, the system identifies the phonological process(es), if any, associated with the user's speech and generates statistics over multiple test targets that can be used to diagnose the user's specific phonological disorders. The system can also be implemented in other contexts such as foreign language instruction and automated attendant applications to cover a wide variety and range of accents and/or phonological disorders.