To compare the three-dimensional changes occurring in the maxillary arch during the use of modified pre-surgical nasoalveolar moulding (PNAM) and Hotz′s plate. A clinical trial including 32 children with unilateral cleft lip and palate (UCLP), 16 treated with Hotz′s plate and 16 with PNAM, was performed. Impressions of the maxillary arches were taken: A. prior to pre-surgical orthopaedics, B. before cheiloplasty and C. after cheiloplasty. Models were digitised using a stereophotogrammetric instrument, and geodesic distances were calculated: anterior, canine and posterior widths of the arch, and lengths and cleft depths of the larger and shorter segments. The time and treatment effects were assessed by two-factor anova. A significant effect of treatment was found for cleft depth at the larger segment: children treated with Hotz′s plate had significantly deeper cleft than children treated with PNAM. All distances significantly changed during time: the anterior and canine widths decreased, while the posterior width, the lengths and depths of the cleft segments increased. Significant treatment per time interactions was found. The anterior and canine widths reduced more with PNAM between time points A and B while Hotz's treatment was more effective between B and C. The shorter segment depth increased more between B and C with PNAM, and between A and B with Hotz's plate. During pre-surgical orthopaedics, therapy with PNAM obtained the best results in reducing the width at the anterior segment of the cleft. This treatment gave a lower increase in cleft depth than treatment with Hotz′s plate.