AbstractObjective:To estimate the prevalence of vitamin A deficiency (VAD) in children and associated risk factors.Design:Analysis of data from a cross-sectional multicentre study performed in the primary care units of the municipalities from January to June 2015. The children’s legal guardians answered a socio-economic questionnaire, and the children’s blood samples were obtained by venipuncture. Plasma retinol was determined by HPLC. Plasma retinol values of <0·70 μmol/l were considered VDA. Poisson multiple regression with robust variance was used. Values of P < 0·05 were considered significant. The data were analysed in the SPSS software, 21.0.Setting:Forty-eight poorest municipalities in the South Region of Brazil.Participants:Children (n 1503) aged 12–59 months.Results:The prevalence of VAD in the sample was 1·9 % (95 % CI (0·5, 6·8)). The following risk factors were associated with the outcome in the final explanatory model: family received Bolsa Familia program benefits (PR = 3·19; 95 % CI (1·69, 6·02)), child was not being breastfed (PR = 5·22; 95 % CI (1·68, 16·18)) and stunting (PR = 4·75; 95 % CI (2·10, 10·73)).Conclusions:VAD did not represent a public health problem for children living in socio-economically vulnerable municipalities in the South Region of Brazil, suggesting a new panorama of this nutritional deficiency even in regions of low socio-economic conditions in these three states. Thus, in view of the current nutritional transition scenario, it is necessary to continuously monitor and improve public policies related to vitamin A supplementation in the country.