Background: It is suggested that dental agenesis affects maxillary protrusion and dental arch relationship in children with unilateral cleft lip and palate (UCLP). In addition, an association between the need for orthognathic surgery and dental agenesis is reported. Aim: The aim was to study the impact of maxillary dental agenesis on craniofacial growth and dental arch relationship in 8-year-old children with UCLP. Subjects and methods: The sample consisted of individuals with UCLP from Scandcleft randomized trials. The participants had available data from diagnosis of maxillary dental agenesis as well as cephalometric measurements (n = 399) and GOSLON assessment (n = 408) at 8 years of age. Results: A statistically significant difference was found for ANB between individuals with agenesis of two or more maxillary teeth (mean 1.52 degrees) in comparison with those with no or only one missing maxillary tooth (mean 3.30 degrees and 2.70 degrees, respectively). Mean NSL/NL was lower among individuals with agenesis of two or more maxillary teeth (mean 9.90 degrees), in comparison with individuals with no or one missing maxillary tooth (mean 11.46 degrees and 11.45 degrees, respectively). The number of individuals with GOSLON score 4-5 was 47.2% in the group with two or more missing maxillary teeth and 26.1% respectively 26.3% in the groups with no or one missing maxillary tooth. No statistically significant difference was found in the comparison between individuals with no agenesis or with agenesis solely of the cleft-side lateral. Conclusion: Maxillary dental agenesis impacts on craniofacial growth as well as dental arch relationship and should be considered in orthodontic treatment planning.