Objective: To determine the prevalence of caries and identify the associated factors among children aged 2 and 4 years in southern Chile. Methods: A cross-sectional study was conducted in a random sample of 2,987 children. Dental examinations were performed in all participating children and a self-administered survey was administered to their primary caregivers. The statistical analysis included a zero inflated negative binomial regression model. Results: The prevalence of caries was 20.3% for 2-year-olds and 52.7% for 4-year-olds. The factors associated with caries included the following: living in the Bio-Bío region, PR2year-old: 1.65 (1.10-2.47), PR4year-old: 1.44 (1.18-1.75) and having a low socioeconomic position, PR2year-old: 5.39 (2.14-13.57), PR4year-old: 3.71 (2.68-5.13) or a medium socioeconomic position, PR2year-old: 2.79 (1.06-7.33), PR4year-old: 2.70 (1.92-3.79). In 4-year-olds, a high frequency of consuming sugary drinks at bedtime (PR: 1.30; 1.06-1.59), not brushing teeth daily (PR: 1.37; 1.18-1.60), and the presence of gingivitis (PR: 1.64; 1.28-2.09) were also associated with caries. Conclusions: The high prevalence of caries in this young group is concerning. The factors associated with caries identified in this study could help in the design of preventive interventions at early ages.