Introduction: Early Childhood Caries (ECC) is a serious public health concern worldwide, especially in communities without water fluoridation. Objective: To determine the prevalence of ECC in 2 and 3 year old children attending rural daycare centers without access to water fluoridation. Methods: A cross-sectional study at community level was performed during 2012. The eligible population was composed of 2 and 3 year-old children from rural daycare centers located in nonfluoridated areas in regions La Araucania, Los Rios, and Los Lagos, Chile. Four calibrated examiners (ICC=0.83) measured the prevalence of dental caries based on criteria proposed by the WHO. Data were analyzed using chi-square test, t-test and logistic regression models. Results: The study sample consisted of 587 children; two-year-olds accounted for 53.32%, and 52.47% were female. Prevalence of ECC was 51.62% with a mean dmft index of 2.53. Region de la Araucania had the highest ECC prevalence (52.79%). Variables that showed association were age, OHI-S and type of health insurance coverage (p<0.05). Conclusion: A high prevalence of ECC was found in areas with a non-fluoridated water supply.