Objective The aim of this cross-sectional study was to investigate the prevalence of dental anomalies in a sample of Egyptian orthodontic patients. Patients and methods This is a retrospective study where 435 digital orthopantograms taken of patients, ranging in age from 14 to 30 years with a mean age of 19 years were studied. The patients were presented for treatment at a private practice in Cairo during the period from 2017 to 2019. The orthopantograms were reviewed for impactions (including and excluding third molars), congenitally missing teeth or hypodontia (including and excluding third molars), ectopic eruption, microdontia (peg-shaped and small-sized maxillary lateral incisors), rudimentary 8's, root dilacerations and supernumerary teeth. Results Excluding third molars, the number of patients that had at least one dental anomaly was 183 or 42.1%. The prevalence of patients with impacted teeth was 66 (15.2%), while the prevalence of congenitally missing teeth was 44 (10.1%). Equal prevalence between males and females was recorded for impacted maxillary permanent canines (M = 16, F = 16) and congenitally missing maxillary permanent canines (M = 1, F = 1). The least prevalence were microdontia (n = 15, 3.4%), dilacerated roots (n = 8, 1.8%) and supernumerary teeth (n = 8, 1.8%). Rudimentary wisdom teeth count was 12 (2.8%) out of the total sample with only maxillary third molars being affected. The prevalence of impacted third molars was 25% (n = 109, M = 27, F = 82). The prevalence of congenitally missing third molars (at least one missing third molar) was 19.3% (n = 84, M = 22, F = 62). Females showed higher prevalence than males for all anomalies except for impacted mandibular permanent canines where males were higher than females (M = 9, F = 5), impacted upper incisors and upper first premolars (M = 1, F = 0) and supernumerary teeth (M = 6, F = 2). The prevalence of patients with impacted permanent second molars was 4.6%. Conclusions Excluding third molars, the most common dental anomaly was impaction followed by teeth agenesis. The most prevalent impaction was the maxillary permanent canine and the most congenitally missing teeth were the maxillary lateral incisors. Root dilacerations and supernumerary teeth were the least common anomalies. Congenitally missing and impacted third molars constitute a large segment of dental anomalies and must be evaluated separately. A large variation exists between the different populations regarding the prevalence of the various anomalies.