Patients with cleft left lip and palate (CLP) normally require extensive surgery from an early age up to the end of adolescence. These surgeries affect the growth of the maxillofacial complex. The degree to which the cleft itself affects growth of the maxillofacial complex remains poorly understood. By analysing the width and elevation of the palatal shelves in unoperated adolescents and adults with unilateral and bilateral cleft lip and palate (UCLP and BCLP, respectively) and a non-cleft control group, it is possible to gain more insight into the real intrinsic growth potential of the maxillary structures. In this study, dental casts of the full permanent dentition of individuals with unrepaired UCLP (n = 68) and BCLP (n = 13) and non-cleft controls (n = 24) from the same area of Indonesia were digitized three-dimensionally. Maxillary arch width in the canine, premolar and molar regions, and the width and elevation of the palatal shelves were measured. Results showed that in patients with UCLP, the width of the palatal shelves on the cleft side in all regions, and on the non-cleft side in the canine/first premolar region, was significantly smaller compared with the control group. BCLP subjects showed similar deviations. In the UCLP group, the palatal shelves were rotated cranially and positioned more vertically. In the BCLP group, the palatal shelves were inclined by almost 10 ° more than the control group. The width of the palatal shelf and width of the maxillary arch positively correlated in the canine and first premolar regions for both the cleft and non-cleft side in patients with UCLP, and in the canine region for patients with BCLP. This means that the wider the palatal shelf, the wider the maxillary arch. The elevation of palatal shelves correlated with the maxillary arch width in all regions in patients with UCLP, and only in the premolar region in the control group. Thus, the wider the arch width, the smaller the elevation angle (the maxillary shelves are less vertical). No correlations between palatal shelf elevation and maxillary arch width were found in the BCLP group. This shows that the intrinsic growth potential in patients with UCLP and BCLP is affected by a smaller palatal shelf width and larger elevation of the shelves. These deviations may result in a wider cleft.