Introduction: Malocclusion results from a combination of dental and skeletal disharmonies. The relationship between the size of maxillary and mandibular teeth is important for achieving a correct occlusion. Tooth size discrepancy (TSD) may play a significant role in the etiology of malocclusion. Many genetic and environmental factors can affect early dental and skeletal development and cause deviations from perfect symmetry. Such small deviations from symmetry can manifest as directional (DA) or fluctuating asymmetry (FA), and both may represent a measure of impaired developmental stability. The increased level of tooth and dental arch asymmetries also contribute to the etiology of malocclusions. An increased genetic susceptibility to environmental stressors can lead to increased developmental instability and elevated levels of FA in various structures such as tooth size and dental arch dimensions. Aim: To compare the degree of dental and dentoalveolar asymmetry (DA and FA) among patients with Class I, II, and III malocclusions and to correlate those asymmetries with intermaxillary tooth size discrepancies or anterior and overall Bolton ratios. Subjects and methods: The samples comprised randomly selected plaster dental casts of 131 patients (39 Class I, mean age 14.9±2.1 (19 males and 20 females), 57 Class II, mean age 14.2±1.4 (23 males and 34 females), and 35 Class III, mean age 17.8±2.9 (20 males and 15 females)] from the Department of Orthodontics, School of Dental Medicine, University of Zagreb, Croatia. Dental models were scanned and digitized using ATOS II SO ("small objects") scanning technology (GoM mbH, Braunschweig, Germany), and 3D virtual objects were created. The measurements of the teeth and dental arch measurements were taken using ATOS viewer version 6.A.2 software. Tooth crown dimensions of 14 teeth in each dental arch were taken. The anterior and overall Bolton ratios were calculated. In each dental arch, six arch widths, five arch depths, and dental arch chords from buccal cusp tips to mesial angle of the central incisor were measured. Directional (DA), fluctuating (FA), and total weighted asymmetries (TWA) were calculated using equations suggested by Palmer and Strobeck (2003). The data were analyzed using SPSS 10.0 software. An analysis of variance (ANOVA) was used to compare differences between the groups. The Pearson's correlations were calculated to test statistically significant associations between the measures of FA and Bolton's ratios. Results: DA of mesio-distal tooth size differs in different malocclusion in both upper and lower arches. It seems that DA follows the pattern of tooth morphogenetic fields. Molars and premolars, as more distal teeth, exhibited the greatest asymmetry in both jaws. In females with Class II malocclusion, DA was more pronounced on the right side in the upper jaw and on the left side in the lower jaw displaying the pattern of crossed asymmetry. In Class III, both males and females displayed a specific pattern of DA. The greatest asymmetry affects second molars and central incisors. Females displayed large dimensions on the right side in both jaws. Regarding the inter-arch differences, the lower teeth seem to be more asymmetrical than the upper teeth. Composite TWA measures of fluctuating asymmetry for dental and dental arch variables were the highest in Class III, and lowest in Class I malocclusion. Males displayed a higher degree of asymmetry than females. The mean values of the Bolton total ratio showed the strongest correlation with TWA of MD tooth size in maxilla (P < 0.01). A significant association of the Bolton’s total and overall ratio and width of lower dental arch was also established (P < 0.02). Conclusion: DA of tooth size and dental arch size were of different sizes and directions in different malocclusions. A specific pattern of crossed asymmetry was observed for tooth size and arch size DA in some malocclusions. The TWA values were low but they differed significantly between the groups of malocclusion. They affected the Bolton’s ratio and may be associated with the etiology of malocclusions. Class III malocclusion displayed higher DA and FA values than Class I and Class II malocclusion. The highest DA and FA in Class III points to the fact that patients with this malocclusion were subjected to higher stress levels (genetic and/or environmental) during early development. Both DA and FA of tooth and dental arch size can be considered possible indicators of developmental instability caused by genetic and/or environmental stress and may contribute to a better assessment of developmental instability in patients with different malocclusions.