The aim of this study was to describe time trends in stunting and obesity in children under five years of age in Alagoas State, Brazil. Two surveys were conducted with representative samples, the first in 1992 (n = 1,228) and the second in 2005 (n = 1,384). Stunting was defined as height-for-age < -2 standard deviations and obesity as weight-for-height > 2 standard deviations. Prevalence of stunting decreased from 22.5% to 11.4% (PR = 0.50; 95%CI: 0.42; 0.60), while obesity increased from 6.7% to 9.3% (PR = 1.36; 95%CI: 1.04; 1.77). During the same period there was a decrease (p ≤ 0.05) in the proportions of the following variables: rural residence, households without running water, households with more than four members, mothers with more than two children, low birth weight, and mother's lack of access to prenatal care. Adjustment for these variables significantly reduced the magnitude of associations, and the 95% confidence included 1.0, suggesting that changes in the prevalence of stunting and obesity were mediated by these characteristics. During the period, there was a striking reduction in the prevalence of stunting and an increase in the frequency of obesity.