Objective: This cross-sectional study was conducted to evaluate if nutritional deficiencies were associated with early childhood caries in a low income population. Methods: It involved 85 children under the age of 71 months enrolled in three day care centers in São Luis- Brazil. Anthropometric parameters (height, weight, body mass index-BMI) were measured following standardized procedures and transformed in Z scores according WHO. The serum markers (hemoglobin, serum iron and ferritin) were analyzed to evaluate the presence of iron deficiency anemia. Results: The prevalence of early childhood caries (ECC) was 36.47% (n = 31) and the dmft was 3.74 (± 2.9). Results of Z score for children with dmft ≥ 1 showed that 30% of them were at risk of malnutrition or malnourished according to the parameters weight / height and BMI/ age. The Poisson regression analysis showed that children with early childhood caries had lower Z scores for weight / height (p = 0.001, coef = 0.64) and BMI / age (p = 0.001, coef = 0.62) and they also had the smallest hemoglobin levels (p = 0.036, coef = 0.66). Conclusion: Early childhood caries was associated with anthropometric and blood markers of nutritional deficiency in the population studied.