Numerous bioarcheological investigations have suggested that as agriculture intensifies, levels of physiological stress and poor health increase. However, previous research in Southeast Asia suggests that a decline in health was not universal. This study aimed to provide the first investigation of human health during the intensification of rice agriculture in the large skeletal sample from the prehistoric site of Ban Non Wat, Northeast Thailand (1750–420 b.c.). Health was analysed using two indicators of childhood stress, the prevalence of linear enamel hypoplasia (LEH), a measure of early childhood stress, and stature, as a measure of late childhood stress, were collated for 190 adults. Sex-specific diachronic relationships between the prevalence of LEH and stature were explored. For both sexes, initially the prevalence of LEH was found to decrease and then increase over time. Stature remained constant over time for males, although for females stature increased initially, then decreased. Early childhood stress was not significantly correlated with stature in females (P = 0.185), but high levels of LEH were unexpectedly correlated with taller male stature (P = 0.017). Our findings suggest an initial improvement in health during agricultural intensification at this site, likely related to a reduction in physiological perturbations and maintenance of a nutritious diet during this time. The subsequent deterioration in health may reflect geomorphologically and archaeologically indicated variation in environmental conditions and consequential sociocultural changes. We suggest that the sex-differences in the relationship between stature and LEH may relate to the timing of stress and/or catch-up growth. Am J Phys Anthropol 153:484–495, 2014. © 2013 Wiley Periodicals, Inc.