Clefts are common birth defects. They are accompanied by various malformations, including disturbances in facial look as well as skeletal disorders that include malocclusions, most frequently crossbites and class III anomalies. The aim of the study was to present the commonest malocclusions in patients with total cleft of the lip, alveolar bone and palate (n = 154) and compare the results to the healthy on-cleft patients (n = 151). Normal occlusion, characteristic for I angle class, was observed in 50% of the control group and 30% of the examined. In the examined patients with clefts, most frequently crossbite and open bite on the cleft side was observed. In patients with clefts, only 2 out of 154 patients presented isolated dental anomalies. In healthy individuals the commonest occlusal disorder was distal occlusion and dental anomalies. The commonest malocclusions among patients with clefts are crossbites and class III malocclusions.