Objectives. To determine the prevalence of vitamin A deficiency (VAD) and nutritional anemia (NA) in children under five in Peru. Materials and methods. Cross-sectional study with a stratified and multi-staged probabilistic sample conducted between November 2007 and April 2010.2,736 children were included for NA and 1,465 children for VAD. NA was defined as Hb<11 g/dL.VAD was identified by serum retinol levels <20 μg/dL. Sociodemographic variables related to the child and the mother were studied in addition to their participation in growth control and development programs, integrated nutrition program and supplementation with iron and vitamin A. Analysis of complex samples was performed, descriptive statistics and logistic regression with 95% confidence intervals and a significance level of p<0.05 were calculated. Results. The prevalence of VAD was 11.7% (95% CI: 9.4 to 14.4). The highest prevalences were in children under five months (44.6%) and those living in rural areas (19.5%). The prevalence of NA was 33% (95% CI: 29.9 to 36.1) and was higher in children under 11 months (68.2%) and children of mothers aged 13-19 years old (55.4 %). Conclusions. VAD is a public health problem that remains, with the most affected children living in rural areas and in the jungle. The prevalence of NA shows a slight improvement. It is necessary to improve the efficiency and impact of programs that include supplementation of vitamin A and iron.