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Cleft Lip and Palate (CLP) is among the most frequent congenital abnormalities. The impaired facial development affects the articulation, with different phonemes being impacted inhomogeneously among different patients. This work focuses on automatic phoneme analysis of children with CLP for a detailed diagnosis and therapy control. In clinical routine, the state-of-the-art evaluation is based on perceptual evaluations. Perceptual ratings act as ground-truth throughout this work, with the goal to build an automatic system that is as reliable as humans. We propose two different automatic systems focusing on modeling the articulatory space of a speaker: one system models a speaker by a GMM, the other system employs a speech recognition system and estimates fMLLR matrices for each speaker. SVR is then used to predict the perceptual ratings. We show that the fMLLR-based system is able to achieve automatic phoneme evaluation results that are in the same range as perceptual inter-rater-agreements.