Background: Primary dentition is a determinant for future permanent occlusion. Objective: This aimed to evaluate the prevalence of malocclusion and associated variables in the primary dentition among preschoolers in the city of Tbilisi, Georgia. Methods: A cross-sectional survey was conducted among kindergarten children aged 3–5 years. Orthodontic characteristics were assessed by one calibrated clinician (E.G). Questionnaires were given to parents to record associated variables like general health problems, functional changes, and the presence of non-nutritive sucking habits. Results: A total of 396 participants aged 3-5 were included in the study. The prevalence of malocclusion was 49.8%, without significant differences among genders. The prevalence of Class II malocclusion was 21.2%(±4.091), followed by a deep overbite, i.e, 10.7% (±3.14), crossbite, i.e, 7% (±2.561), anterior open bite, i.e, 6.9%, and Class III malocclusion, i.e, 1.6% (±1.513). A total of 41.5% of children with breathing problems had Class II and 13% had crossbite. Speech disorder in 46.8% of cases was associated with anterior open bite. Pacifier users had Class II in 22.5%, deep overbite in 12.2%, and open bite in 9.2% of cases. There was a high prevalence of anterior open bite (25.2%) in children with a thumb-sucking habit (RR=4.90). These data sets are statistically reliable (p < 0.05). Conclusion: Almost half of the evaluated preschoolers had malocclusion. The most frequent disorder was Class II. Malocclusion is associated with non-nutritive sucking habits and mouth breathing.