Background. Breastfeeding has multiple nutritional, immunological and psychological benefits, as well as a positive influence on the development of the stomatognathic system. Objectives. The present study attempted to determine the relationship between the duration of breastfeeding and the development of non-nutritive habits, and transversal and vertical occlusal alterations in preschool children. Material and methods. This cross-sectional study involved 155 preschoolers aged 2–5 years from 3 public schools in Lima, Peru. The sample was divided into 2 groups with regard to the duration of breast-feeding: group A (n = 50) included infants that had been breastfed for up to 6 months; and group B (n = 105) included infants that had been breastfed for 6–12 months. Two trained and calibrated dentists evaluated each group, and clinically determined the presence or absence of transversal or vertical occlusal alterations. Likewise, the children’s parents or caregivers were consulted to determine the development of non-nutritive habits. Results. A significant association was found between breastfeeding duration and the development of the oral breathing habit; groups A and B showed a prevalence of 30.0% and 16.2%, respectively (p = 0.048). Likewise, breastfeeding duration affected the appearance of oral breathing (OR (odds ratio) = 0.84; 95% CI (confidence interval): 0.74–0.96; p = 0.011). Furthermore, the use of a bottle for more than 24 months significantly influenced the appearance of oral habits (OR = 3.55; 95% CI: 1.20–10.55; p = 0.022) and open bite (OR = 12.12; 95% CI: 1.16–126.31; p = 0.037). Conclusions. Breastfeeding duration of 6–12 months was shown to be a protective factor in preventing the appearance of oral breathing. Posterior crossbite (PCB), open bite and deep bite seemed not to be influenced by breastfeeding duration. However, the use of a bottle for more than 24 months significantly influenced the appearance of anterior open bite.