To evaluate the effect of chronic malnutrition on the oral health of children aged 1 to 5 years. An observational, analytical, cross-sectional study was conducted and involved 82 children (12–71 months of age). Nutritional status was evaluated using anthropometric indicators and oral health status/caries prevalence was measured. Non-stimulated saliva was collected and flow rate and buffering capacity was measured. The mean dmft index was 1.38 for the adequately nourished children, 3.04 for those with mild malnutrition, 2.5 for those with moderate malnutrition and 2.4 for those with severe malnutrition. 69 of the 82 children had low to very low buffering capacity. No significant differences among the groups were found between malnutrition and age, buffering capacity or the dmft index ( P > .05). However, significant differences in salivary flow were found among the different malnutrition categories ( P < .05). Spearman correlation coefficient revealed a weak negative correlation between nutrition and salivary flow (r = −0.267). Malnutrition exerts a negative impact on the oral cavity of children and a reduction in salivary flow rate was observed with the increase in malnutrition. Diagnosing the effects of malnutrition in oral environment of children is important because it could improve the quality of life and give them an adequate treatment.