This study aimed to evaluate the malocclusions of patients with a cleft lip and/or palate (CLP) and to compare malocclusion characteristics between subjects with a pre-foramen incisor cleft (PIC) and a trans-foramen incisor cleft (TIC). A cross-sectional study was conducted of 117 cleft patients (53 per cent male) aged 6-37 years (mean age 14.7 ± 7.4 years) who attended the Dental Specialty Center in the city of Fortaleza, Brazil, between 2004 and 2007. Oral clefts were classified and radiographic examinations and dental casts were analysed to determine malocclusions and facial patterns. Malocclusion measurements were compared between the PIC and TIC groups by Mann-Whitney and Fisher's exact tests. The percentage of subjects with PIC, TIC, post-foramen incisor cleft, and rare cleft were 20.5, 73.5, 5.1, and 0.9 per cent, respectively. The prevalence of malocclusions in subjects with a CLP was 82.1 per cent (molar relationships Classes II and III) in 6- to 12-year-olds, and a severe malocclusion [dental aesthetic index (DAI)] was observed in all patients aged 13 years and above. The frequency of patients with a normal canine relationship, open bite, and anterior crossbite was higher in the PIC group than in the TIC group (6-12 years). Patients aged 13 years and above in the PIC group showed lower means for the largest anterior maxillary irregularity, higher means for positive anterior mandibular overjet, a lower frequency of crowding in the anterior incisal segments, and a normal antero-posterior molar relationship compared with the TIC group. Severe malocclusions were prevalent in subjects with a CLP. Subjects with a TIC have higher prevalence of malocclusions than those with a PIC.