Aim: The prevalence of dental anomalies in different ethnic groups is different. The aim of this study was to evaluate the prevalence of dental anomalies associated with different malocclusions in Yazd. Iran. Methods: In this retrospective study the census method was used (with the confidence interval of 95% and the error margin of 5%). Dental records of 450 orthodontic patients referred to dental school of Shahid Sadoughi University of Yazd, Iran between 2010 and 2015 were collected. Dental records were classified into skeletal class I, II and III malocclusions (based on ANB angle measurements on cephalograms) searching for dental anomalies related to number, size and position. Data were analyzed using t-test, ANOVA and chi-square tests. Results: A total of 405 patients, (251 females 62%, 154 males 38%) with the mean age of 15.5 ± 4.1 were assessed. 49% of patients had at least one anomaly. The most frequent anomaly was impaction (24.9%). Hypodontia was found in 14.5% of patients and mandibular wisdom tooth was the most commonly missing tooth. 2.9% of patients had supernumerary which the maxillary anterior presented the higher number of it. The frequency of dental anomalies was not different between males and females. There was no correlation between type of malocclusion and frequency of dental anomalies except for hypodontia which was significantly higher in class I malocclusion.Conclusion: The most common anomaly seen in patients referred to the school of dentistry was impaction.