The purpose of this study was to compare the maxillary arch morphology in 5-year-old children treated for unilateral cleft lip and palate (UCLP) with early gingivoplasty (EGP) and without this procedure (non-EGP). Three-dimensional (3-D) imaging was used to verify which measurements and to what degree specific orthodontic parameters differ in both groups. The study included 120 non-syndromic 4.5-5.5-year-old children treated surgically at the age of 6-18 months. Fifty-six children underwent EGP utilising a Skoog-type of technique. The (non-EGP) group consisted of 64 patients. Patients in both groups were treated without nasoalveolar moulding prior to cleft lip repair. The maxillary arch models were obtained and subjected to the 3-D computer-aided imaging procedure and metric analysis. Ten selected orthodontic measurements were calculated based on imaging landmarks. The computed data derived from models in both (EGP and non-EGP) groups were compared. The differences between groups were statistically analysed using Student's test. Five orthodontic measurements: the angle of the lesser segment inclination, dental arch radius of this segment, anterior palatal depth, palatal surface and length of dental arch demonstrate more severe maxillary underdevelopment in patients with previous EGP. The results reaffirm the negative impact of EGP with wide undermining of periosteal flaps on maxillary development and suggest that these five parameters may be the most sensitive early indicators of growth alteration.