Objectives. To assess the association between violence against women inflicted by their partner and the prevalence of chronic malnutrition in their children less than five years old. Materials and methods. A secondary cross-sectional analysis of the 2001 Peru Demographic and Health Survey performed in Peru, with national representativeness. The dependent variable was chronic malnutrition in the youngest child under five years old. The independent variables were emotional violence, physical violence (mild or severe) and sexual violence self-report; the violence was inflicted by the mother's last partner or spouse in the last 12 months. Univariate and multivariate analysis was performed, generalized linear models (log-binomial regression) were used, and the nature of the sample was taken into account. Models for socio-demographic and mother-son health variables were adjusted. Prevalence ratios (PR) and confidence intervals were calculated. Results. Data from 5,154 mothers and children were analyzed. The prevalence of chronic malnutrition was 19.8% (CI 95%: 18.1-21.6). In the multivariate analysis, a higher prevalence of chronic malnutrition was found in the children whose mothers had a history of severe physical violence history: PR=1.27% (IC 95%: 1.09-1.48). There was no evidence of association between the prevalence of chronic malnutrition and other kinds of violence inflicted by a partner. Conclusions. The mothers' report of physical violence in the last year was associated with an increased prevalence of chronic malnutrition in children under five years old.