Poor water quality and under nutrition are important factors affecting the health of many communities in developing countries. The aims of this study were: i) to describe the fluoride water concentration and the hydrogeological conditions in a region of a state located in the central in Mexico ii) to measure the association between undernutrition and dental fluorosis in children living in communities with different drinking water fluoride concentrations in a state located in the central region of Mexico. METHODS Field work was performed in the region to identify the prevailing groundwater flow characteristics and water wells were sampled to analyze water fluoride concentration. Children were selected from three communities that had different drinking water fluoride concentrations (i.e., 0.56, 0.70 and 1.60 mg/l). Fluoridated salt was available in these communities. The Thylstrup-Fejerskov Index (TFI) was used to assess dental fluorosis. Categories four or higher of this index involve changes in the entire tooth surface (ITF ≥ 4). The weight and height of the children were measured. The assessment of undernutrition was based on the World Health Organization criteria: children were classified as being at risk of low-height (Height-for-Age Z score < − 1.0 SD) and having low-height (Height-for-Age Z score < − 2.0 SD) for age and sex, the same cutoff points of the Z score were used to classify "risk of low-weight" and" low-weight children". RESULTS In the region the mineralization of the water captured by the wells is the result of a reaction with volcanic materials. The water fluoride concentration in the region ranged from 0.2 to 1.6 mg/l. A total of 734 schoolchildren participated in the study. The percentage of children in fluorosis categories (ITF ≥ 4) was 15.9%, 21.1% of the children were at risk of low height-for-age, and 8.0% had low height-for-age. The percentage of children with fluorosis (ITF ≥ 4) was 6.3%, 9.1% and 31.9% (p ˂ 0.001) and low high-for-age was 2.9%, 2.5% and 8.4% (p ˂ 0.001), for the communities with F concentrations of 0.56 mg/l, 0.70 mg/l and 1.6 mg/l, respectively. The logistic regression model showed an association between dental fluorosis (TFI ≥ 4) and low height-for-age (OR 2.09, p = 0.022) after adjusting for sex, number of teeth erupted, source of drinking water, use of fluoridated toothpaste and tap water fluoride concentration in the community. CONCLUSIONS Children with low height-for-age were more likely to have dental fluorosis in the TFI categories that affect the entire tooth surface. The results suggest that subpopulations with chronic undernutrition are more susceptible to dental fluorosis.