Objective To examine trends in stunting and overweight in Peruvian children, using 2006 WHO Multicentre Growth Reference Study criteria. Design Trend analyses using nationally representative cross-sectional surveys from Demographic and Health Surveys (1991-2011). We performed logistic regression analyses of stunting and overweight trends in sociodemographic groups (sex, age, urban-rural residence, region, maternal education and household wealth), adjusted for sampling design effects (strata, clusters and sampling weights). Setting Peru. Subjects Children aged 0-59 months surveyed in 1991-92 (n 7999), 1996 (n 14 877), 2000 (n 11 754), 2007-08 (n 8232) and 2011 (n 8186). Results Child stunting declined (F(1, 5149) = 174·8, P ≤ 0·00) and child overweight was stable in the period 1991-2011 (F(1, 5147) = 0·4, P ≤ 0·54). Over the study period, levels of stunting were highest in rural compared with urban areas, the Andean and Amazon regions compared with the Coast, among children of low-educated mothers and among children living in households in the poorest wealth quintile. The trend in overweight rose among males in coastal areas (F(1, 2250) = 4·779, P ≤ 0·029) and among males in the richest wealth quintile (F(1, 1730) = 5·458, P ≤ 0·020). Conclusions The 2011 levels of stunting and overweight were eight times and three and a half times higher, respectively, than the expected levels from the 2006 WHO growth standards. The trend over the study period in stunting declined in most sociodemographic subgroups. The trend in overweight was stable in most sociodemographic subgroups.