The education system in Peru and many other developing countries faces several challenges, including improving education achievement and increasing education enrollment in high school. It is clear from several indicators that rural students have lower education outcomes than do urban students. In this study we used cross-sectional and longitudinal analysis to determine the relationship between height-for-age z-scores (HAZ), weight-for-age z-scores (WAZ), body-mass index (BMI), and education outcomes. The sample was composed of students from 20 elementary public schools in two rural zones in Peru. The descriptive results show that there was no association between any of the anthropometric variables and achievement (mathematics and reading comprehension) or advancing to high school without repeating a grade. However, BMI was associated with dropping out of school: children with higher BMI in 1998 were more likely to be out of school by 2001. The hierarchical multivariate analysis also showed no relationship between anthropometry and achievement at the individual level, but students with relatively higher HAZ in 1998 were more likely to be drop-outs by 2001. These results contradict prior findings that showed a positive association between anthropometric variables (especially HAZ) and education achievement. The results might be explained by the fact that the study was carried out at very poor sites, at altitudes between 3000 and 3500 meters above sea level. The scarce studies about development in high altitudes suggest that the patterns for height and weight for children and adolescents are different than at sea level. Another possible explanation has to do with the fact that in the contexts studied, children who are perceived as relatively heavier (BMI) or taller (HAZ) might be expected to be out of school and start working (in fact, this was the primary reason given by children for dropping out of school).