BackgroundGuatemala suffered from civil war and high levels of inequality and childhood stunting in the second half of the 20th century, but little is known about inequalities in secular trends in adiposity.ObjectivesTo investigate differences in childhood body mass index (BMI) and skinfold thickness trajectories from 1979 to 1999 between three groups of children: High socioeconomic position (SEP) Ladino, Low SEP Ladino, and Low SEP Indigenous Maya.MethodsThe sample comprised 19 346 children aged 7–17 years with 54 638 observations. The outcomes were height, BMI, triceps skinfold thickness (TST), and subscapular skinfold thickness (SST) Z‐scores according to the Centers for Disease Control and Prevention (CDC) references. Sex‐specific multilevel models were used to estimate and compare mean trajectories from 1979 to 1999 between the three groups.ResultsMean Z‐scores were always highest for High SEP Ladino children and lowest for Low SEP Maya children. Despite their very short stature, the Low SEP groups had SST trajectories that were above the 50th centile. The BMI trajectories were relatively flat and within one major centile band of the CDC median, with differences between the three groups that were small (0.2–0.3 Z‐scores) and did not attenuate over time. Conversely, the TST Z‐score trajectories demonstrated larger positive secular trends (e.g., from −1.25 in 1979 to −0.06 in 1999 for Low SEP Maya boys), with differences between the three groups that were large (0.5–1.2 Z‐scores) and did attenuate over time (in boys). Secular trends and between‐group difference in the SST Z‐score trajectories were less pronounced, but again we found stronger evidence in boys that the estimated inequalities attenuated over time.ConclusionsSecular trends and inequalities in skinfolds differ from those for BMI in Guatemalan children. Differences between groups in skinfolds attenuated over time, at least in boys, but whether this is good news is questionable given the very short stature yet relatively large subscapular skinfolds of the Low SEP groups.