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The aim of this cohort study was to quantify the morphological changes in the palatal cleft and true cleft areas with passive plate therapy using a new analysis method based on three-dimensional standardized reproducible landmarks. Forty-five casts of 15 consecutive patients with complete unilateral cleft lip and palate were laser scanned and investigated retrospectively. The landmarks and the coordinate system were defined, and the interrater and intrarater measurement errors were within 1.0 mm. The morphological changes of the cleft palate area after a period of 8 months of passive plate therapy without prior lip surgery are presented graphically. The median decrease in cleft width was 38.0% for the palatal cleft, whereas it was 44.5% for the true cleft. The width of the true and palatal cleft decreased significantly over a period of 8 months. The true cleft area decreased by 34.7% from a median of 185.4 mm² (interquartile range, IQR = 151.5–220.1) to 121.1 mm² (IQR = 100.2–144.6). The palatal cleft area decreased by 31.5% from a median of 334 mm² (IQR = 294.9–349.8) to 228.8 mm². The most important clinical considerations are the reproducibility and reliability of the anatomical points, as well as the associated morphological changes. We propose using the vomer edge to establish a validated measuring method for the width, area, and height of the true cleft.