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Background: Individuals with cleft lip and palate have many anatomic and functional alterations compromising esthetics, hearing, speech, occlusion, and development/craniofacial growth. The rehabilitative treatment of these patients is very challenging and starts at birth aiming at the best treatment for all functional demands. This study aimed to evaluate the dimensional alterations of the dental arches of neonates with cleft lip and palate after two different primary surgical techniques. Materials and Methods: The sample comprised 114 digital models of children aged from 3 to 36 months, with unilateral complete cleft lip and palate divided into two groups. Two different phases were evaluated: precheiloplasty and 1 year after palatoplasty. The evaluation was performed through the digital models of each child obtained by scanning digitalization (3D Scanner). Dental arches measurements were accomplished through Appliance Designer software. The following measurements were assessed: dental arch area, anterior amplitude of the cleft, total length of dental arch, intercanine distance, and intertuberosity distance. t-test was applied to compare differences between groups. Results: No statistically significant differences were observed between groups at precheiloplasty phase. At 1 year after palatoplasty, the groups differed in the total length of dental arch (P = 0.002), with greater values for Group I. Conclusion: This study suggests that the results of the different surgical techniques may alter the growth and development of the dental arches of neonates with cleft lip and palate.