There are conflicting reports on a possible association between body mass index (BMI) and caries. Given the ongoing worldwide increase in obesity, we undertook a 5-year follow-up study on 201 Mexican schoolchildren to analyse their BMI and dental caries experience. The children’s weight and height were recorded, and their BMI was calculated using the WHO tables. Decayed, missing, and filled surfaces in both dentitions (dmf/DMFS) were assessed annually according to WHO criteria by two calibrated researchers (Kappa value 0.92 p < 0.001). The means, standard deviation, an ANOVA, and Student’s t-test were calculated to analyse the relationship between the variables. At baseline, the children had an average of 6.5 ± 0.5 years, a BMI of 17.2 ± 3.1 (CI95% 16.8–17.6). Their weight’s classifications were 61% normal, 19% obese, 17% overweight, and 3% showed thinness. At the end of the study, their BMI were 20.6 ± 4.4 (CI95% 19.8–21.5), 53% normal, 15% obese, 30% overweight, and 2% thin. The children’s dmfs decreased from 5.8 ± 9.2 to 1.8 ± 3.4 and the DMFS increased from 0.07 ± 05 to 1.4 ± 2.3. In this population based on a 5-year follow-up, caries prevalence and incidence were not significantly associated with the BMI. However, schoolchildren with malnutrition had the highest caries indexes.